U.S. patent application number 11/009635 was filed with the patent office on 2005-09-22 for methods and composition for the production of orthogonal trna-aminoacyltrna synthetase pairs.
This patent application is currently assigned to The Scripps Research Institute. Invention is credited to Anderson, John Christopher, Chin, Jason W., Liu, David R., Magliery, Thomas J., Meggers, Eric L., Mehl, Ryan Aaron, Pastrnak, Miro, Santoro, Stephen William, Schultz, Peter, Wang, Lei, Zhang, Zhiwen.
Application Number | 20050208536 11/009635 |
Document ID | / |
Family ID | 26962950 |
Filed Date | 2005-09-22 |
United States Patent
Application |
20050208536 |
Kind Code |
A1 |
Schultz, Peter ; et
al. |
September 22, 2005 |
Methods and composition for the production of orthogonal
tRNA-aminoacyltRNA synthetase pairs
Abstract
This invention provides compositions and methods for generating
components of protein biosynthetic machinery including orthogonal
tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs
of tRNAs/synthetases. Methods for identifying orthogonal pairs are
also provided. These components can be used to incorporate
unnatural amino acids into proteins in vivo.
Inventors: |
Schultz, Peter; (La Jolla,
CA) ; Wang, Lei; (San Diego, CA) ; Anderson,
John Christopher; (San Diego, CA) ; Chin, Jason
W.; (Cambridge, GB) ; Liu, David R.;
(Lexington, MA) ; Magliery, Thomas J.; (North
Haven, CT) ; Meggers, Eric L.; (Philadelphia, PA)
; Mehl, Ryan Aaron; (Lancaster, PA) ; Pastrnak,
Miro; (San Diego, CA) ; Santoro, Stephen William;
(Cambridge, MA) ; Zhang, Zhiwen; (San Diego,
CA) |
Correspondence
Address: |
QUINE INTELLECTUAL PROPERTY LAW GROUP, P.C.
P O BOX 458
ALAMEDA
CA
94501
US
|
Assignee: |
The Scripps Research
Institute
La Jolla
CA
|
Family ID: |
26962950 |
Appl. No.: |
11/009635 |
Filed: |
December 10, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11009635 |
Dec 10, 2004 |
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10126931 |
Apr 19, 2002 |
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60285030 |
Apr 19, 2001 |
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60355514 |
Feb 6, 2002 |
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Current U.S.
Class: |
435/6.12 ;
435/199; 435/252.3; 435/320.1; 435/6.1; 435/69.1; 536/23.2 |
Current CPC
Class: |
C07K 14/505 20130101;
C12P 21/02 20130101; C12P 19/26 20130101; C12P 13/22 20130101; A61P
7/00 20180101; C12P 13/00 20130101; C12N 9/93 20130101; C12N 15/67
20130101; C07K 14/00 20130101; C12P 21/00 20130101; C12P 13/04
20130101; A61P 43/00 20180101; C12P 13/005 20130101 |
Class at
Publication: |
435/006 ;
435/069.1; 435/199; 435/252.3; 435/320.1; 536/023.2 |
International
Class: |
C12Q 001/68; C07H
021/04; C12N 009/22; C12N 001/21; C12N 015/74 |
Goverment Interests
[0002] The invention was made with United States Government support
under Grant No. 6502573 from the Office of Naval Research and Grant
No. GM2159 from the National Institutes. The United States
Government has certain rights in the invention.
Claims
1. A composition comprising an orthogonal aminoacyl-tRNA synthetase
(O-RS), wherein the O-RS preferentially aminoacylates an orthogonal
tRNA (O-tRNA) with an unnatural amino acid.
2. The composition of claim 1, wherein the O-RS comprises an amino
acid sequence selected from the group consisting of: SEQ ID NO:
35-66.
3. The composition of claim 1, wherein the O-RS aminoacylates the
O-tRNA with the unnatural amino acid in vivo.
4. The composition of claim 1, wherein the unnatural amino acid is
selected from the group consisting of: an O-methyl-L-tyrosine, an
L-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, an
O-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, a
tri-O-acetyl-GlcNAc.beta.-- serine, an L-Dopa, a fluorinated
phenylalanine, an isopropyl-L-phenylalani- ne, a
p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a
p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a
phosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine,
a p-amino-L-phenylalanine, and an isopropyl-L-phenylalanine.
5. The composition of claim 1, wherein the unnatural amino acid is
selected from the group consisting of: an unnatural analogue of a
tyrosine amino acid; an unnatural analogue of a glutamine amino
acid; an unnatural analogue of a phenylalanine amino acid; an
unnatural analogue of a serine amino acid; an unnatural analogue of
a threonine amino acid; an alkyl, aryl, acyl, azido, cyano, halo,
hydrazine, hydrazide, hydroxyl, alkenyl, alkynl, ether, thiol,
sulfonyl, seleno, ester, thioacid, borate, boronate, phospho,
phosphono, phosphine, heterocyclic, enone, imine, aldehyde,
hydroxylamine, keto, or amino substituted amino acid, or any
combination thereof; an amino acid with a photoactivatable
cross-linker; a spin-labeled amino acid; a fluorescent amino acid;
an amino acid with a novel functional group; an amino acid that
covalently or noncovalently interacts with another molecule; a
metal binding amino acid; a metal-containing amino acid; a
radioactive amino acid; a photocaged amino acid, a
photoisomerizable amino acid; a biotin or biotin-analogue
containing amino acid; a glycosylated or carbohydrate modified
amino acid; a keto containing amino acid; an amino acid comprising
polyethylene glycol; an amino acid comprising polyether; a heavy
atom substituted amino acid; a chemically cleavable or
photocleavable amino acid; an amino acid with an elongated side
chain; an amino acid containing a toxic group; a sugar substituted
amino acid; a sugar substituted serine; a carbon-linked
sugar-containing amino acid; a redox-active amino acid; an
.alpha.-hydroxy containing acid; an amino thio acid containing
amino acid; an .alpha.,.alpha. disubstituted amino acid; a
.beta.-amino acid; and a cyclic amino acid other than proline.
6. The composition of claim 1, wherein the O-RS has one or more
improved or enhanced enzymatic properties, selected from the groups
consisting of: K.sub.m, and K.sub.cat, for the unnatural amino acid
as compared to a natural amino acid.
7. A polypeptide comprising an amino acid sequence encoded by a
coding polynucleotide sequence, the coding polynucleotide sequence
selected from the group consisting of: a) a coding polynucleotide
sequence that encodes a polypeptide selected from SEQ ID NO:35-66;
b) a polynucleotide sequence which hybridizes under highly
stringent conditions over substantially an entire length of a
polynucleotide sequence of (a); and, c) a complementary sequence of
(a), or (b).
8. The polypeptide of claim 7, wherein the encoded polypeptide
encodes an orthogonal aminoacyl tRNA sythetase.
9. A polypeptide comprising an amino acid sequence selected from
SEQ ID NO:35-66.
10-16. (canceled)
17. A composition comprising an orthogonal tRNA (O-tRNA), wherein
the O-tRNA recognizes a selector codon and wherein the O-tRNA is
preferentially aminoacylated with an unnatural amino acid by an
orthogonal aminoacyl-tRNA synthetase, the composition comprising
the orthogonal aminoacyl-tRNA synthetase (O-RS).
18. The composition of claim 17, wherein the O-tRNA and the O-RS
are complementary.
19. The composition of claim 17, wherein the composition comprises
a mutRNATyr-mutTyrRS pair.
20. The composition of claim 19, wherein the composition comprises
a mutRNATyr-SS12TyrRS pair.
21. The composition of claim 17, wherein the composition comprises
a mutRNALeu-mutLeuRS pair.
22. The composition of claim 17, wherein the composition comprises
a mutRNAThr-mutThrRS pair.
23. The composition of claim 17, wherein the composition comprises
a mutRNAGlu-mutGluRS pair
24. The composition of claim 17, wherein the O-tRNA and the O-RS
are derived by mutation of a naturally occurring tRNA and an RS
from at least one organism, wherein the at least one organism is a
prokaryotic organism.
25. The composition of claim 24, wherein the at least one organism
is selected from the group consisting of: Methanococcus jannaschii,
Methanobacterium thernoautotrophicum, and Halobacterium.
26. The composition of claim 17, wherein the O-tRNA and the O-RS
are derived by mutation of a naturally occurring tRNA and RS from
at least one organism, wherein the at least one organism is a
eukaryotic organism.
27. The composition of claim 26, wherein the at least one organism
is selected from the group consisting of: yeasts, mammals, fungi,
insects, plants and protists.
28. The composition of claim 17, wherein the O-tRNA is derived by
mutation of a naturally occurring tRNA from a first organism and
the O-RS is derived by mutation of a naturally occurring RS from a
second organism.
29. The composition of claim 17, wherein the O-tRNA and the O-RS
are isolated from at least one organism, wherein the at least one
organism is a prokaryotic organism.
30. The composition of claim 29, wherein the at least one organism
is selected from the group consisting of: Methanococcus jannaschii,
Methanobacterium thermoautotrophicum, and Halobacterium.
31. The composition of claim 17, wherein the O-tRNA and the O-RS
are isolated from at least one organism, wherein the at least one
organism is a eukaryotic organism.
32. The composition of claim 31, wherein the at least one organism
is selected from the group consisting of: yeasts, mammals, fungi,
insects, plants and protists.
33. The composition of claim 17, wherein the O-tRNA is isolated
from a first organism and the O-RS is isolated from a second
organism.
34. The composition of claim 17, wherein one or more of the O-tRNA
and the O-RS is isolated from one or more library, which one or
more library comprises an O-tRNA or an O-RS from one or more
organism.
35. The composition of claim 34, wherein the one or more organism
comprises a prokaryote or a eukaryote.
36. The composition of claim 17, wherein the composition is in a
cell.
37. The composition of claim 17, wherein the composition comprises
an in vitro translation system.
38-73. (canceled)
74. A recombinant ORS produced by a method, the method comprising:
(a) generating a library of variant RS molecules derived from at
least one aminoacyl-tRNA synthetase (RS) from a first organism; (b)
selecting or screening the library of variant RSs for members that
aminoacylate an orthogonal tRNA (O-tRNA) in the presence of an
unnatural amino acid or a natural amino acid, thereby providing a
pool of active RSs; and, (c) selecting or screening the pool of
active RS to identify active RSs that preferentially aminoacylate
the O-tRNA in the absence of the unnatural amino acid, thereby
identifying at least one member of the pool that is specific for
the unnatural amino acid, providing the at least one recombinant
O-RS; wherein the at least one recombinant O-RS preferentially
aminoacylates the O-tRNA with the unnatural amino acid.
75-115. (canceled)
116. The recombinant ORS of claim 74, wherein the method comprises
negatively selecting members of the pool that preferentially
aminoacylate the O-tRNA in the absence of the unnatural amino
acid.
117. The recombinant ORS of claim 74, wherein the method comprises
positively selecting those members of the pool that do not
aminoacylate the O-tRNA in the absence of the unnatural amino
acid.
118. The composition of claim 1, wherein the unnatural amino acid
is selected from the group consisting of: O-allyl-L-tyrosine,
para-substituted L-tyrosine wherein the substitution comprises a
saturated or unsaturated hydrocarbon, GlcNAc-serine,
p-iodo-L-phenylalanine, p-bromo-L-phenylalanine,
3,4-dihydroxy-L-phenylal- anine, p-acetyl-L-phenylalanine,
m-acetyl-L-phenylalanine, and 4-(2-oxo-propoxy)-L-phenylalanine.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. provisional patent
application Ser. No. 60/285,030, filed Apr. 19, 2001, and U.S.
patent application Ser. No. 60/355,514, filed Feb. 6, 2002, the
specifications of which are incorporated herein in their
entirety.
FIELD OF THE INVENTION
[0003] The invention relates to the field of translation
biochemistry. In particular, the invention relates to methods for
producing mutated orthogonal tRNAs, mutated orthogonal
aminoacyl-tRNA synthetases, and pairs thereof. The invention also
provides methods for identifying orthogonal pairs, which are used
for the incorporation of unnatural amino acids into proteins in
vivo, and related compositions.
BACKGROUND OF THE INVENTION
[0004] Proteins carry out virtually all of the complex processes of
life, from photosynthesis to signal transduction and the immune
response. To understand and control these intricate activities, a
better understanding of the relationship between the structure and
function of proteins is needed.
[0005] Unlike small organic molecule synthesis wherein almost any
structural change can be made to influence functional properties of
a compound, the synthesis of proteins is limited to changes encoded
by the twenty natural amino acids. The genetic code of every known
organism, from bacteria to human, encodes the same twenty common
amino acids. These amino acids can be modified by
post-translational modification of proteins, e.g., glycosylation,
phosphorylation or oxidation, or in rarer instances, by the
enzymatic modification of aminoacylated suppressor tRNAs, e.g., in
the case of selenocysteine. Nonetheless, polypeptides, which are
synthesized from only these 20 simple building blocks, carry out
all of the complex processes of life.
[0006] Both site-directed and random mutagenesis, in which specific
amino acids in a protein can be replaced with any of the other
nineteen common amino acids, have become important tools for
understanding the relationship between the structure and function
of proteins. These methodologies have made possible the generation
of proteins with enhanced properties, including stability,
catalytic activity and binding specificity. Nevertheless, changes
in proteins are limited to the 20 common amino acids, most of which
have simple functional groups. See Knowles, J. R. Tinkering with
enzymes: what are we learning? Science, 236:1252-1258 (1987); and,
Zoller, M. J., Smith, M. Oligonucleotide-directed mutagenesis of
DNA fragments cloned into M13 vectors, Methods Enzymol, 100:468-500
(1983). By expanding the genetic code to include additional amino
acids with novel biological, chemical or physical properties, the
properties of proteins, e.g., the size, acidity, nucleophilicity,
hydrogen-bonding, hydrophobic properties, etc., can be modified as
compared to a protein composed of only amino acids from the 20
common amino acids, e.g., as in a naturally occurring protein.
[0007] Several strategies have been employed to introduce unnatural
amino acids into proteins. The first experiments involved the
derivatization of amino acids with reactive side-chains such as
Lys, Cys and Tyr, for example, the conversion of lysine to
N.sup..epsilon.-acetyl-lysine. Chemical synthesis also provides a
straightforward method to incorporate unnatural amino acids, but
routine solid-phase peptide synthesis is generally limited to small
peptides or proteins with less than 100 residues. With the recent
development of enzymatic ligation and native chemical ligation of
peptide fragments, it is possible to make larger proteins, but such
methods are not easily scaled. See, e.g., P. E. Dawson and S. B. H.
Kent, Annu. Rev. Biochem., 69:923 (2000). A general in vitro
biosynthetic method in which a suppressor tRNA chemically acylated
with the desired unnatural amino acid is added to an in vitro
extract capable of supporting protein biosynthesis, has been used
to site-specifically incorporate over 100 unnatural amino acids
into a variety of proteins of virtually any size. See, e.g., V. W.
Cornish, D. Mendel and P. G. Schultz, Angew. Chem. Int. Ed. Engl.,
1995, 34:621 (1995); C. J. Noren, S. J. Anthony-Cahill, M. C.
Griffith, P. G. Schultz, A general method for site-specific
incorporation of unnatural amino acids into proteins, Science 244
182-188 (1989); and, J. D. Bain, C. G. Glabe, T. A. Dix, A. R.
Chamberlin, E. S. Diala, Biosynthetic site-specific incorporation
of a non-natural amino acid into a polypeptide, J. Am. Chem. Soc.
111 8013-8014 (1989). A broad range of functional groups has been
introduced into proteins for studies of protein stability, protein
folding, enzyme mechanism, and signal transduction. Although these
studies demonstrate that the protein biosynthetic machinery
tolerates a wide variety of amino acid side chains, the method is
technically demanding, and yields of mutant proteins are low.
[0008] Over 50 years ago, it was found that many analogs of natural
amino acids inhibit the growth of bacteria. Analysis of the
proteins produced in the presence of these amino acid analogs
revealed that they had been substituted for their natural
counterparts to various extents. See, e.g., M. H. Richmond,
Bacteriol. Rev., 26:398 (1962). This occurs because the
aminoacyl-tRNA synthetase, the enzyme responsible for the
attachment of the correct amino acid to its cognate tRNA, cannot
rigorously distinguish the analog from the corresponding natural
amino acid. For instance, norleucine is charged by methionyl-tRNA
synthetase, and p-fluorophenylalanine is charged by
phenylalanine-tRNA synthetase. See, D. B. Cowie, G. N. Cohen, E. T.
Bolton and H. de Robichon-Szulmajster, Biochim. Biophys. Acta,
1959, 34:39 (1959); and, R. Munier and G. N. Cohen, Biochim.
Biophys. Acta. 1959, 31:378 (1959).
[0009] An in vivo method, termed selective pressure incorporation,
was later developed to exploit the promiscuity of wild-type
synthetases. See, e.g., N. Budisa, C. Minks, S. Alefelder, W.
Wenger, F. M. Dong, L. Moroder and R. Huber, FASEB J., 13:41
(1999). An auxotrophic strain, in which the relevant metabolic
pathway supplying the cell with a particular natural amino acid is
switched off, is grown in minimal media containing limited
concentrations of the natural amino acid, while transcription of
the target gene is repressed. At the onset of a stationary growth
phase, the natural amino acid is depleted and replaced with the
unnatural amino acid analog. Induction of expression of the
recombinant protein results in the accumulation of a protein
containing the unnatural analog. For example, using this strategy,
o, m and p-fluorophenylalanines have been incorporated into
proteins, and exhibit two characteristic shoulders in the UV
spectrum which can be easily identified, see, e.g., C. Minks, R.
Huber, L. Moroder and N. Budisa, Anal. Biochem., 284:29 (2000);
trifluoromethionine has been used to replace methionine in
bacteriophage .lambda. lysozyme to study its interaction with
chitooligosaccharide ligands by .sup.19F NMR, see, e.g., H. Duewel,
E. Daub, V. Robinson and J. F. Honek, Biochemistry, 36:3404 (1997);
and trifluoroleucine has been inserted in place of leucine,
resulting in increased thermal and chemical stability of a
leucine-zipper protein. See, e.g. Y. Tang, G. Ghirlanda, W. A.
Petka, T. Nakajima, W. F. DeGrado and D. A. Tirrell, Angew. Chem.
Int. Ed. Engl., 40:1494 (2001). Moreover, selenomethionine and
telluromethionine are incorporated into various recombinant
proteins to facilitate the solution of phases in X-ray
crystallography. See, e.g., W. A. Hendrickson, J. R. Horton and D.
M. Lemaster, EMBO J. 9:1665 (1990); J. O. Boles, K. Lewinski, M.
Kunkle, J. D. Odom, B. Dunlap, L. Lebioda and M. Hatada, Nat.
Struct. Biol., 1:283 (1994); N. Budisa, B. Steipe, P. Demange, C.
Eckerskorn, J. Kellermann and R. Huber, Eur. J. Biochem., 230:788
(1995); and, N. Budisa, W. Karnbrock, S. Steinbacher, A. Humm, L.
Prade, T. Neuefeind, L. Moroder and R. Huber, J. Mol. Biol.,
270:616 (1997). Methionine analogs with alkene or alkyne
functionalities have also been inserted efficiently, allowing for
additional modification of proteins by chemical means. See, e.g.,
J. C. M. van Hest and D. A. Tirrell, FEBS Lett., 428:68 (1998); J.
C. M. van Hest, K. L. Kiick and D. A. Tirrell, J. Am. Chem. Soc.,
122:1282 (2000); and, K. L. Kiick and D. A. Tirrell, Tetrahedron,
56:9487 (2000).
[0010] The success of this method depends on the recognition of the
unnatural amino acid analogs by aminoacyl-tRNA synthetases, which,
in general, requires high selectivity to insure the fidelity of
protein translation. Therefore, the range of chemical functionality
accessible via this route is limited. For instance, although
thiaproline can be incorporated quantitatively into proteins,
oxaproline and selenoproline cannot. See, N. Budisa, C. Minks, F.
J. Medrano, J. Lutz, R. Huber and L. Moroder, Proc. Natl. Acad.
Sci. USA, 95:455 (1998). One way to expand the scope of this method
is to relax the substrate specificity of aminoacyl-tRNA
synthetases, which has been achieved in a limited number of cases.
For example, it was found that replacement of Ala.sup.294 by Gly in
Escherichia coli phenylalanyl-tRNA synthetase (PheRS) increases the
size of substrate binding pocket, and results in the acylation of
tRNAPhe by p-Cl-phenylalanine (p-Cl-Phe). See, M. Ibba, P. Kast and
H. Hennecke, Biochemistry, 33:7107 (1994). An Escherichia coli
strain harboring this mutant PheRS allows the incorporation of
p-Cl-phenylalanine or p-Br-phenylalanine in place of phenylalanine.
See, e.g., M. Ibba and H. Hennecke, FEBS Lett., 364:272 (1995);
and, N. Sharma, R. Furter, P. Kast and D. A. Tirrell, FEBS Lett.,
467:37 (2000). Similarly, a point mutation Phe130Ser near the amino
acid binding site of Escherichia coli tyrosyl-tRNA synthetase was
shown to allow azatyrosine to be incorporated more efficiently than
tyrosine. See, F. Hamano-Takaku, T. Iwama, S. Saito-Yano, K.
Takaku, Y. Monden, M. Kitabatake, D. Soll and S. Nishimura, J.
Biol. Chem., 275:40324 (2000).
[0011] The fidelity of aminoacylation is maintained both at the
level of substrate discrimination and proofreading of non-cognate
intermediates and products. Therefore, an alternative strategy to
incorporate unnatural amino acids into proteins in vivo is to
modify synthetases that have proofreading mechanisms. These
synthetases cannot discriminate and therefore activate amino acids
that are structurally similar to the cognate natural amino acids.
This error is corrected at a separate site, which deacylates the
mischarged amino acid from the tRNA to maintain the fidelity of
protein translation. If the proofreading activity of the synthetase
is disabled, structural analogs that are misactivated may escape
the editing function and be incorporated. This approach has been
demonstrated recently with the valyl-tRNA synthetase (ValRS). See,
V. Doring, H. D. Mootz, L. A. Nangle, T. L. Hendrickson, V. de
Crecy-Lagard, P. Schimmel and P. Marliere, Science, 292:501 (2001).
ValRS can misaminoacylate tRNAVal with Cys, Thr, or aminobutyrate
(Abu); these noncognate amino acids are subsequently hydrolyzed by
the editing domain. After random mutagenesis of the Escherichia
coli chromosome, a mutant Escherichia coli strain was selected that
has a mutation in the editing site of ValRS. This edit-defective
ValRS incorrectly charges tRNAVal with Cys. Because Abu sterically
resembles Cys (--SH group of Cys is replaced with --CH3 in Abu),
the mutant ValRS also incorporates Abu into proteins when this
mutant Escherichia coli strain is grown in the presence of Abu.
Mass spectrometric analysis shows that about 24% of valines are
replaced by Abu at each valine position in the native protein.
[0012] At least one major limitation of the methods described above
is that all sites corresponding to a particular natural amino acid
throughout the protein are replaced. The extent of incorporation of
the natural and unnatural amino acid may also vary--only in rare
cases can quantitative substitution be achieved since it is
difficult to completely deplete the cognate natural amino acid
inside the cell. Another limitation is that these strategies make
it difficult to study the mutant protein in living cells, because
the multi-site incorporation of analogs often results in toxicity.
Finally, this method is applicable in general only to close
structural analogs of the common amino acids, again because
substitutions must be tolerated at all sites in the genome.
[0013] Solid-phase synthesis and semi-synthetic methods have also
allowed for the synthesis of a number of small proteins containing
novel amino acids. For example, see the following publications and
references cited within: Crick, F. J. C., Barrett; L. Brenner, S.
Watts-Tobin, R. General nature of the genetic code for proteins.
Nature, 192:1227-1232 (1961); Hofmann, K., Bohn, H. Studies on
polypeptides. XXXVI. The effect of pyrazole-imidazole replacements
on the S-protein activating potency of an S-peptide fragment, J.
Am. Chem., 5914-5919 (1966); Kaiser, E. T. Synthetic approaches to
biologically active peptides and proteins including enzymes, Acc.
Chem. Res., 47-54 (1989); Nakatsuka, T., Sasaki, T., Kaiser, E. T.
Peptide segment coupling catalyzed by the semisynthetic enzyme
thiosubtilisin, J. Am. Chem. Soc., 109:3808-3810 (1987); Schnolzer,
M., Kent, S B H. Constructing proteins by dovetailing unprotected
synthetic peptides: backbone-engineered HIV protease, Science,
256(5054):221-225 (1992); Chaiken, I. M. Semisynthetic peptides and
proteins, CRC Crit. Rev. Biochem., 11(3):255-301 (1981); Offord, R.
E. Protein engineering by chemical means? Protein Eng.,
1(3):151-157 (1987); and, Jackson, D. Y., Burnier, J., Quan, C.,
Stanley, M., Tom, J., Wells, J. A. A Designed Peptide Ligase for
Total Synthesis of Ribonuclease A with Unnatural Catalytic
Residues, Science, 266(5183):243-247 (1994).
[0014] Chemical modification has been used to introduce a variety
of unnatural side chains, including cofactors, spin labels and
oligonucleotides into proteins in vitro. See, e.g., Corey, D. R.,
Schultz, P. G. Generation of a hybrid sequence-specific
single-stranded deoxyribonuclease, Science, 283(4832):1401-1403
(1987); Kaiser, E. T., Lawrence D. S., Rokita, S. E. The chemical
modification of enzymatic specificity, Rev. Biochem., 54:565-595
(1985); Kaiser, E. T., Lawrence, D. S. Chemical mutation of enzyme
active sites, Science, 226(4674):505-511 (1984); Neet, K. E., Nanci
A, Koshland, D. E. Properties of thiol-subtilisin, J. Biol. Chem.,
243(24):6392-6401 (1968); Polgar, L. B., M. L. A new enzyme
containing a synthetically formed active site. Thiol-subtilisin. J.
Am. Chem. Soc., 88:3153-3154 (1966); and, Pollack, S. J., Nakayama,
G. Schultz, P. G. Introduction of nucleophiles and spectroscopic
probes into antibody combining sites, Science, 242(4881):1038-1040
(1988).
[0015] Alternatively, biosynthetic methods that employ chemically
modified aminoacyl-tRNAs have been used to incorporate several
biophysical probes into proteins synthesized in vitro. See the
following publications and references cited within: Brunner, J. New
Photolabeling and crosslinking methods, Annu. Rev. Biochem.,
62:483-514 (1993); and, Krieg, U. C., Walter, P., Hohnson, A. E.
Photocrosslinking of the signal sequence of nascent preprolactin of
the 54-kilodalton polypeptide of the signal recognition particle,
Proc. Natl. Acad. Sci, 83(22):8604-8608 (1986).
[0016] Previously, it has been shown that unnatural amino acids can
be site-specifically incorporated into proteins in vitro by the
addition of chemically aminoacylated suppressor tRNAs to protein
synthesis reactions programmed with a gene containing a desired
amber nonsense mutation. Using these approaches, one can substitute
a number of the common twenty amino acids with close structural
homologues, e.g., fluorophenylalanine for phenylalanine, using
strains auxotrophic for a particular amino acid. See, e.g., Noren,
C. J., Anthony-Cahill, Griffith, M. C., Schultz, P. G. A general
method for site-specific incorporation of unnatural amino acids
into proteins, Science, 244:182-188 (1989); M. W. Nowak, et al.,
Science 268:439-42 (1995); Bain, J. D., Glabe, C. G., Dix, T. A.,
Chamberlin, A. R., Diala, E. S. Biosynthetic site-specific
Incorporation of a non-natural amino acid into a polypeptide, J.
Am. Chem. Soc., 111:8013-8014 (1989); N. Budisa et al., FASEB J.
13:41-51 (1999); Ellman, J. A., Mendel, D., Anthony-Cahill, S.,
Noren, C. J., Schultz, P. G. Biosynthetic method for introducing
unnatural amino acids site-specifically into proteins, Methods in
Enz., 301-336 (1992); and, Mendel, D., Cornish, V. W. &
Schultz, P. G. Site-Directed Mutagenesis with an Expanded Genetic
Code, Annu. Rev. Biophys. Biomol. Struct. 24, 435-62 (1995).
[0017] For example, a suppressor tRNA was prepared that recognized
the stop codon UAG and was chemically aminoacylated with an
unnatural amino acid. Conventional site-directed mutagenesis was
used to introduce the stop codon TAG, at the site of interest in
the protein gene. See, e.g., Sayers, J. R., Schmidt, W. Eckstein,
F. 5', 3' Exonuclease in phosphorothioate-based
oligonucleotide-directed mutagenesis, Nucleic Acids Res.,
16(3):791-802 (1988). When the acylated suppressor tRNA and the
mutant gene were combined in an in vitro transcription/translation
system, the unnatural amino acid was incorporated in response to
the UAG codon which gave a protein containing that amino acid at
the specified position. Experiments using [.sup.3H]-Phe and
experiments with .alpha.-hydroxy acids demonstrated that only the
desired amino acid is incorporated at the position specified by the
UAG codon and that this amino acid is not incorporated at any other
site in the protein. See, e.g., Noren, et al, supra; and, Ellman,
J. A., Mendel, D., Schultz, P. G. Site-specific incorporation of
novel backbone structures into proteins, Science, 197-200
(1992).
[0018] In general, these in vitro approaches are limited by
difficulties in achieving site-specific incorporation of the amino
acids, by the requirement that the amino acids be simple
derivatives of the common twenty amino acids or problems inherent
in the synthesis of large proteins or peptide fragments.
[0019] Microinjection techniques have also been use incorporate
unnatural amino acids into proteins. See, e.g., M. W. Nowak, P. C.
Kearney, J. R. Sampson, M. E. Saks, C. G. Labarca, S. K. Silverman,
W. G. Zhong, J. Thorson, J. N. Abelson, N. Davidson, P. G. Schultz,
D. A. Dougherty and H. A. Lester, Science, 268:439 (1995); and, D.
A. Dougherty, Curr. Opin. Chem. Biol., 4:645 (2000). A Xenopus
oocyte was coinjected with two RNA species made in vitro: an mRNA
encoding the target protein with a UAG stop codon at the amino acid
position of interest and an amber suppressor tRNA aminoacylated
with the desired unnatural amino acid. The translational machinery
of the oocyte then inserted the unnatural amino acid at the
position specified by UAG. This method has allowed in vivo
structure-function studies of integral membrane proteins, which are
generally not amenable to in vitro expression systems. Examples
include the incorporation of a fluorescent amino acid into
tachykinin neurokinin-2 receptor to measure distances by
fluorescence resonance energy transfer, see, e.g., G. Turcatti, K.
Nemeth, M. D. Edgerton, U. Meseth, F. Talabot, M. Peitsch, J.
Knowles, H. Vogel and A. Chollet, J. Biol. Chem., 271:19991 (1996);
the incorporation of biotinylated amino acids to identify
surface-exposed residues in ion channels, see, e.g., J. P.
Gallivan, H. A. Lester and D. A. Dougherty, Chem. Biol., 4:739
(1997); the use of caged tyrosine analogs to monitor conformational
changes in an ion channel in real time, see, e.g., J. C. Miller, S.
K. Silverman, P. M. England, D. A. Dougherty and H. A. Lester,
Neuron, 20:619 (1998); and, the use of .alpha.-hydroxy amino acids
to change ion channel backbones for probing their gating
mechanisms, see, e.g., P. M. England, Y. Zhang, D. A. Dougherty and
H. A. Lester, Cell, 96:89 (1999); and, T. Lu, A. Y. Ting, J.
Mainland, L. Y. Jan, P. G. Schultz and J. Yang, Nat. Neurosci.,
4:239 (2001).
[0020] However, there are limitations microinjection method, e.g.,
the suppressor tRNA has to be chemically aminoacylated with the
unnatural amino acid in vitro, and the acylated tRNA is consumed as
a stoichiometric reagent during translation and cannot be
regenerated. This limitation results in poor suppression efficiency
and low protein yields, necessitating highly sensitive techniques
to assay the mutant protein, such as electrophysiological
measurements. Moreover, this method is only applicable to cells
that can be microinjected.
[0021] The ability to incorporate unnatural amino acids directly
into proteins in vivo offers the advantages of high yields of
mutant proteins, technical ease, the potential to study the mutant
proteins in cells or possibly in living organisms and the use of
these mutant proteins in therapeutic treatments. The ability to
include unnatural amino acids with various sizes, acidities,
nucleophilicities, hydrophobicities, and other properties into
proteins can greatly expand our ability to rationally and
systematically manipulate the structures of proteins, both to probe
protein function and create new proteins or organisms with novel
properties. However, the process is difficult, because the complex
nature of tRNA-synthetase interactions that are required to achieve
a high degree of fidelity in protein translation. Therefore,
improvements to the process are needed to provide more efficient
and effective methods to alter the biosynthetic machinery of the
cell. The present invention addresses these and other needs, as
will be apparent upon review of the following disclosure.
SUMMARY OF THE INVENTION
[0022] The present invention provides compositions of components
used in protein biosynthetic machinery, which include orthogonal
tRNA-aminoacyl-tRNA synthetase pairs and the individual components
of the pairs. Methods for generating and selecting orthogonal
tRNAs, orthogonal aminoacyl-tRNA synthetases, and pairs thereof
that can use an unnatural amino acid are also provided.
Compositions of the invention include novel orthogonal
tRNA-aminoacyl-tRNA synthetase pairs, e.g., mutRNATyr-mutTyrRS
pairs, mutRNALeu-mutLeuRS pairs, mutRNAThr-mutThrRS pairs,
mutRNAGlu-mutGluRS pairs, and the like. The novel orthogonal pairs
can be use to incorporate an unnatural amino acid in a polypeptide
in vivo. Other embodiments of the invention include selecting
orthogonal pairs.
[0023] Compositions of the present invention include an orthogonal
aminoacyl-tRNA synthetase (O-RS), where the O-RS preferentially
aminoacylates an orthogonal tRNA (O-tRNA) with an unnatural amino
acid, optionally, in vivo. In one embodiment, the O-RS comprises a
nucleic acid comprising a polynucleotide sequence selected from the
group consisting of: SEQ ID NO: 4-34 (see, Table 5) and a
complementary polynucleotide sequence thereof. In another
embodiment, the O-RS has improved or enhanced enzymatic properties,
e.g., the K.sub.m is higer or lower, the k.sub.cat is higher or
lower, the value of k.sub.cat/K.sub.m is higher or lower or the
like, for the unnatural amino acid compared to a naturally
occurring amino acid, e.g., one of the 20 known amino acids.
[0024] The unnatural amino acids of the present invention encompass
a variety of substances. For example, they optionally include (but
are not limited to) such molecules as: an O-methyl-L-tyrosine, an
L-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, an
O-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, a
tri-O-acetyl-GlcNAc.beta.-- serine, an L-Dopa, a fluorinated
phenylalanine, an isopropyl-L-phenylalani- ne, a
p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a
p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a
phosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine,
a p-amino-L-phenylalanine, and an isopropyl-L-phenylalanine.
Additionally, other examples optionally include (but are not
limited to) an unnatural analogue of a tyrosine amino acid; an
unnatural analogue of a glutamine amino acid; an unnatural analogue
of a phenylalanine amino acid; an unnatural analogue of a serine
amino acid; an unnatural analogue of a threonine amino acid; an
alkyl, aryl, acyl, azido, cyano, halo, hydrazine, hydrazide,
hydroxyl, alkenyl, alkynl, ether, thiol, sulfonyl, seleno, ester,
thioacid, borate, boronate, phospho, phosphono, phosphine,
heterocyclic, enone, imine, aldehyde, hydroxylamine, keto, or amino
substituted amino acid, or any combination thereof; an amino acid
with a photoactivatable cross-linker; a spin-labeled amino acid; a
fluorescent amino acid; an amino acid with a novel functional
group; an amino acid that covalently or noncovalently interacts
with another molecule; a metal binding amino acid; a
metal-containing amino acid; a radioactive amino acid; a photocaged
amino acid; a photoisomerizable amino acid; a biotin or
biotin-analogue containing amino acid; a glycosylated or
carbohydrate modified amino acid; a keto containing amino acid; an
amino acid comprising polyethylene glycol; an amino acid comprising
polyether; a heavy atom substituted amino acid; a chemically
cleavable or photocleavable amino acid; an amino acid with an
elongated side chain; an amino acid containing a toxic group; a
sugar substituted amino acid, e.g., a sugar substituted serine or
the like; a carbon-linked sugar-containing amino acid; a
redox-active amino acid; an .alpha.-hydroxy containing acid; an
amino thio acid containing amino acid; an .alpha.,.alpha.
disubstituted amino acid; a .beta.-amino acid; and a cyclic amino
acid other than proline.
[0025] The present invention also includes a polypeptide comprising
an amino acid sequence encoded by a coding polynucleotide sequence
which is selected from: a coding polynucleotide sequence selected
from SEQ ID NO: 4-34 (see, Table 5 for sequences); a coding
polynucleotide sequence encoding a polypeptide selected from SEQ ID
NO: 35-66 a polynucleotyide sequence which hybridizes under highly
stringent conditions over substantially the entire length of such
polynucleotide sequences; and complementary sequences of any of
such sequences. Additionally, such polypeptide optionally encodes
an orthogonal aminoacyl tRNA sythetase and/or an amino acid
sequence selected from SEQ ID NO:35 to SEQ ID NO:66.
[0026] The present invention also includes a nucleic acid
comprising a polynucleotide sequence selected from the group
consisting of: a polynucleotide sequence selected from SEQ ID NO:1
to SEQ ID NO:3 (or a complementary polynucleotide sequence thereof)
and a polynucleotide sequence which hybridizes under highly
stringent conditions over substantially the entire length of such
polynucleotide sequences. Such nucleic acids also include wherein
the polynucleotide sequence comprises an orthogonal tRNA and/or
wherein the polynucleotide sequence forms a complementary pair with
an orthogonal aminoacyl-tRNA synthetase (which optionally is
selected from the those whose sequence is listed in SEQ ID NO:35 to
SEQ ID NO:66.
[0027] Compositions of an orthogonal tRNA (O-tRNA) are also
included, where the O-tRNA recognizes a selector codon and wherein
the O-tRNA is preferentially aminoacylated with an unnatural amino
acid by an orthogonal aminoacyl-tRNA synthetase. In one embodiment,
the O-tRNA comprises a nucleic acid comprising a polynucleotide
sequence selected from the group consisting of: SEQ ID NO:1-3 (see,
Table 5) and a complementary polynucleotide sequence thereof.
[0028] Selector codons of the present invention expand the genetic
codon framework of protein biosynthetic machinery. For example, a
selector codon includes, e.g., a unique three base codon (composed
of natural or unnatural bases), a nonsense codon (such as a stop
codon, e.g., an amber codon, or an opal codon), an unnatural codon,
a rare codon, a codon comprising at least four bases, a codon
comprising at least five bases, a codon comprising at least six
bases, or the like.
[0029] In one embodiment, the O-tRNA (optionally comprising within
compositions) can include an orthogonal aminoacyl-tRNA synthetase
(O-RS), e.g., where the O-tRNA and the O-RS are complementary,
e.g., an O-tRNA/O-RS pair. In one embodiment, a pair comprises
e.g., a mutRNATyr-mutTyrRS pair, such as mutRNATyr-SS12TyrRS pair,
a mutRNALeu-mutLeuRS pair, a mutRNAThr-mutThrRS pair, a
mutRNAGlu-mutGluRS pair, or the like. In another embodiment, the
pair is other than a mutRNAGln-mutGlnRS derived from Escherichia
coli, a mutRNAAsp-mutAspRS derived from yeast or a
mutRNAPheCUA-mutphenlalanineRS from yeast, where these pairs do not
possess the properties of the pairs of the present invention.
[0030] The O-tRNA and the O-RS can be derived by mutation of a
naturally occurring tRNA and RS from a variety of organisms. In one
embodiment, the O-tRNA and O-RS are derived from at least one
organism, where the organism is a prokaryotic organism, e.g.,
Methanococcus jannaschii, Methanobacterium thermoautotrophicum,
Halobacterium, Escherichia coli, A. fulgidus, P. furiosus, P.
horikoshii, A. pernix, T. thermophilus, or the like. Optionally,
the organism is a eukaryotic organism, e.g., plants (e.g., complex
plants such as monocots, or dicots), algea, fungi (e.g., yeast,
etc), animals (e.g., mammals, insects, arthropods, etc.), insects,
protists, or the like. Optionally, the O-tRNA is derived by
mutation of a naturally occurring tRNA from a first organism and
the O-RS is derived by mutation of a naturally occurring RS from a
second organism. In one embodiment, the O-tRNA and O-RS can be
derived from a mutated tRNA and mutated RS.
[0031] The O-tRNA and the O-RS also can optionally be isolated from
a variety of organisms. In one embodiment, the O-tRNA and O-RS are
isolated from at least one organism, where the organism is a
prokaryotic organism, e.g., Methanococcus jannaschii,
Methanobacterium thermoautotrophicum, Halobacterium, Escherichia
coli, A. fulgidus, P. furiosus, P. horikoshii, A. pernix, T.
thermophilus, or the like. Optionally, the organism is a eukaryotic
organism, e.g., plants (e.g., complex plants such as monocots, or
dicots), algea, fungi (e.g., yeast, etc), animals (e.g., mammals,
insects, arthropods, etc.), insects, protists, or the like.
Optionally, the O-tRNA is isolated from a naturally occurring tRNA
from a first organism and the O-RS is isolated from a naturally
occurring RS from a second organism. In one embodiment, the O-tRNA
and O-RS can be isolated from one or more library (which optionally
comprises one or more O-tRNA and/or O-RS from one or more organism
(including those comprising prokaryotes and/or eukaryotes).
[0032] In another aspect, the compositions of the present invention
can be in a cell. Optionally, the compositions of the present
invention can be in an in vitro translation system.
[0033] Methods for generating components of the protein
biosynthetic machinery, such as O-RSs, O-tRNAs, and orthogonal
O-tRNA/O-RS pairs that can be used to incorporate an unnatural
amino acid are provided in the present invention. Methods for
selecting an orthogonal tRNA-tRNA synthetase pair for use in in
vivo translation system of an organism are also provided. The
unnatural amino acids and selectors codons used in the methods are
described above and below.
[0034] Methods for producing at least one recombinant orthogonal
aminoacyl-tRNA synthetase (O-RS) comprise: (a) generating a library
of (optionally mutant) RSs derived from at least one aminoacyl-tRNA
synthetase (RS) from a first organism, e.g., a prokaryotic
organism, such as Methanococcus jannaschii, Methanobacterium
thermoautotrophicum, Halobacterium, Escherichia coli, A. fulgidus,
P. furiosus, P. horikoshii, A. pernix, T. thermophilus, or the
like; (b) selecting (and/or screening) the library of RSs
(optionally mutant RSs) for members that aminoacylate an orthogonal
tRNA (O-tRNA) in the presence of an unnatural amino acid and a
natural amino acid, thereby providing a pool of active (optionally
mutant) RSs; and/or, (c) selecting (optionally through negative
selection) the pool for active RSs (e.g., mutant RSs) that
preferentially aminoacylate the O-tRNA in the absence of the
unnatural amino acid, thereby providing the at least one
recombinant O-RS; wherein the at least one recombinant O-RS
preferentially aminoacylates the O-tRNA with the unnatural amino
acid. Recombinant O-RSs produced by the methods are also included
in the present invention.
[0035] In one embodiment, the RS is an inactive RS. The inactive RS
can be generated by mutating an active RS. For example, the
inactive RS can be generated by mutating at least about 1, at least
about 2, at least about 3, at least about 4, at least about 5, at
least about 6, or at least about 10 or more amino acids to
different amino acids, e.g., alanine.
[0036] Libraries of mutant RSs can be generated using various
mutagenesis techniques known in the art. For example, the mutant
RSs can be generated by site-specific mutations, random mutations,
diversity generating recombination mutations, chimeric constructs,
and by other methods described herein or known in the art.
[0037] In one embodiment, selecting (and/or screening) the library
of RSs (optionaly mutant RSs) for members that are active, e.g.,
that aminoacylate an orthogonal tRNA (O-tRNA) in the presence of an
unnatural amino acid and a natural amino acid, includes:
introducing a positive selection or screening marker, e.g., an
antibiotic resistance gene, or the like, and the library of
(optionally mutant) RSs into a plurality of cells, wherein the
positive selection and/or screening marker comprises at least one
selector codon, e.g., an amber, ochre, or opal codon; growing the
plurality of cells in the presence of a selection agent;
identifying cells that survive (or show a specific response) in the
presence of the selection and/or screening agent by suppressing the
at least one selector codon in the positive selection or screening
marker, thereby providing a subset of positively selected cells
that contains the pool of active (optionally mutant) RSs.
Optionally, the selection and/or screening agent concentration can
be varied.
[0038] In one aspect, the positive selection marker is a
chloramphenicol acetyltransferase (CAT) gene and the selector codon
is an amber stop codon in the CAT gene. Optionally, the positive
selection marker is a .beta.-lactamase gene and the selector codon
is an amber stop codon in the .beta.-lactamase gene. In another
aspect the positive screening marker comprises a fluorescent or
luminescent screening marker or an affinity based screening marker
(e.g., a cell surface marker).
[0039] In one embodiment, negatively selecting or screening the
pool for active RSs (optionally mutants) that preferentially
aminoacylate the O-tRNA in the absence of the unnatural amino acid
includes: introducing a negative selection or screening marker with
the pool of active (optionally mutant) RSs from the positive
selection or screening into a plurality of cells of a second
organism, wherein the negative selection or screening marker
comprises at least one selector codon (e.g., an antibiotic
resistance gene, e.g., a chloramphenicol acetyltransferase (CAT)
gene); and, identifying cells that survive or show a specific
screening response in a 1st media supplemented with the unnatural
amino acid and a screening or selection agent, but fail to survive
or to show the specific response in a 2nd media not supplemented
with the unnatural amino acid and the selection or screening agent,
thereby providing surviving cells or screened cells with the at
least one recombinant O-RS. For example, a CAT identification
protocol optionally acts as a positive selection and/or a negative
screening in determination of appropriate O-RS recombinants. For
instance, a pool of clones is optionally replicated on growth
plates containing CAT (which comprises at least one selctor codon)
either with or without one or more unnatural amino acid. Colonies
growing exclusively on the plates containing unnatural amino acids
are thus regarded as containing recombinant O-RS. In one aspect,
the concentration of the selection (and/or screening) agent is
varied. In some aspects the first and second organisms are
different. Thus, the first and/or second organism optionally
comprises: a prokaryote, a eukaryote, a mammal, an Escherichia
coli, a fungi, a yeast, an archaebacterium, a eubacterium, a plant,
an insect, a protist, etc. In other embodiments, the screening
marker comprises a fluorescent or luminescent screening marker or
an affinity based screening marker.
[0040] In another embodiment, screening or selecting (e.g.,
negatively selecting) the pool for active (optionally mutant) RSs
includes: isolating the pool of active mutant RSs from the positive
selection step (b); introducing a negative selection or screening
marker, wherein the negative selection or screening marker
comprises at least one selector codon (e.g., a toxic marker gene,
e.g., a ribonuclease barnase gene, comprising at least one selector
codon), and the pool of active (optionally mutant) RSs into a
plurality of cells of a second organism; and identifying cells that
survive or show a specific screening response in a 1st media not
supplemented with the unnatural amino acid, but fail to survive or
show a specific screening response in a 2nd media supplemented with
the unnatural amino acid, thereby providing surviving or screened
cells with the at least one recombinant O-RS, wherein the at least
one recombinant O-RS is specific for the unnatural amino acid. In
one aspect, the at least one selector codon comprises about two or
more selector codons. Such embodiments optionally can include
wherein the at least one selector codon comprises two or more
selector codons, and wherein the first and second organism are
different (e.g., each organism is optionally, e.g., a prokaryote, a
eukaryote, a mammal, an Escherichia coli, a fungi, a yeast, an
archaebacteria, a eubacteria, a plant, an insect, a protist, etc.).
Also, some aspects include wherein the negative selction marker
comprises a ribonuclease barnase gene (which comprises at least one
selector codon). Other aspects include wherein the screening marker
optionally comprises a fluorescent or luminescent screening marker
or an affinity based screening marker. In the embodiments herein,
the screenings and/or selections optionally include variation of
the screening and/or selection stringency.
[0041] In one embodiment, the methods for producing at least one
recombinant orthogonal aminoacyl-tRNA synthetase (O-RS) can further
comprise: (d) isolating the at least one recombinant O-RS; (e)
generating a second set of O-RS (optionally mutated) derived from
the at least one recombinant O-RS; and, (f) repeating steps (b) and
(c) until a mutated O-RS is obtained that comprises an ability to
preferentially aminoacylate the O-tRNA. Optionally, steps (d)-(f)
are repeated, e.g., at least about two times. In one aspect, the
second set of mutated O-RS derived from at least one recombinant
O-RS can be generated by mutagenesis, e.g., random mutagenesis,
site-specific mutagenesis, recombination or a combination
thereof.
[0042] The stringency of the selection/screening steps, e.g., the
positive selection/screening step (b), the negative
selection/screening step (c), or both the positive and negative
selection/screening steps (b) and (c), in the above-described
methods, optionally includes varying the selection/screening
stringency. In another embodiment, the positive selection/screening
step (b), the negative selection/screening step (c) or both the
positive and negative selection/screening steps (b) and (c)
comprise using a reporter, wherein the reporter is detected by
fluorescence-activated cell sorting (FACS) or wherein the reporter
is detected by luminescence. Optionally, the reporter is displayed
on a cell surface, on a phage display or the like and selected
based upon affinity or catalytic activity involving the unnatural
amino acid or an analogue. In one embodiment, the mutated
synthetase is displayed on a cell surface, on a phage display or
the like.
[0043] The methods embodied herein optionally comprise wherein the
unnatural amino acid is selected from, e.g.: an
O-methyl-L-tyrosine, an L-3-(2-naphthyl)alanine, a
3-methyl-phenylalanine, an O-4-allyl-L-tyrosine, a
4-propyl-L-tyrosine, a tri-O-acetyl-GlcNAc.beta.-- serine, an
L-Dopa, a fluorinated phenylalanine, an isopropyl-L-phenylalani-
ne, a p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a
p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a
phosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine,
a p-amino-L-phenylalanine, and an isopropyl-L-phenylalanine. A
recombinant O-RS produced by the methods herein is also included in
the current invention.
[0044] Methods for producing a recombinant orthogonal tRNA (O-tRNA)
include: (a) generating a library of mutant tRNAs derived from at
least one tRNA, e.g., a suppressor tRNA, from a first organism; (b)
selecting (e.g., negatively selecting) or screening the library for
(optionally mutant) tRNAs that are aminoacylated by an
aminoacyl-tRNA synthetase (RS) from a second organism in the
absence of a RS from the first organism, thereby providing a pool
of tRNAs (optionally mutant); and, (c) selecting or screening the
pool of tRNAs (optionally mutant) for members that are
aminoacylated by an introduced orthogonal RS(O-RS), thereby
providing at least one recombinant O-tRNA; wherein the at least one
recombinant O-tRNA recognizes a selector codon and is not
efficiency recognized by the RS from the second organism and is
preferentially aminoacylated by the O-RS. In some embodiments the
at least one tRNA is a suppressor tRNA and/or comprises a unique
three base codon of natural and/or unnatural bases, or is a
nonsense codon, a rare codon, an unnatural codon, a codon
comprising at least 4 bases, an amber codon, an ochre codon, or an
opal stop codon. In one embodiment, the recombinant O-tRNA
possesses an improvement of orthogonality. It will be appreciated
that in some embodiments, O-tRNA is optionally imported into a
first organism from a second organism without the need for
modification. In various embodiments, the first and second
organisms are either the same or different and are optionally
chosen from, e.g., prokaryotes (e.g., Methanococcus jannaschii,
Methanobacteium thermoautotrophicum, Escherichia coli,
Halobacterium, etc.), eukaryotes, mammals, fungi, yeasts,
archaebacteria, eubacteria, plants, insects, protists, etc.
Additionally, the recombinant tRNA is optionally aminoacylated by
an unnatrual amino acid, wherein the unnatural amino acid is
biosynthesized in vivo either naturally or through genetic
manipulation. The unnatural amino acid is optionally added to a
growth medium for at least the first or second organism.
[0045] In one aspect, selecting (e.g., negatively selecting) or
screening the library for (optionally mutant) tRNAs that are
aminoacylated by an aminoacyl-tRNA synthetase (step (b)) includes:
introducing a toxic marker gene, wherein the toxic marker gene
comprises at least one of the selector codons (or a gene that leads
to the production of a toxic or static agent or a gene esential to
the organism wherein such marker gene comprises at least one
selector codon) and the library of (optionally mutant) tRNAs into a
plurality of cells from the second organism; and, selecting
surviving cells, wherein the surviving cells contain the pool of
(optionally mutant) tRNAs comprising at least one orthogonal tRNA
or nonfunctional tRNA. For example, surviving cells can be selected
by using a comparison ratio cell density assay.
[0046] In another aspect, the toxic marker gene can include two or
more selector codons. In another embodiment of the methods, the
toxic marker gene is a ribonuclease barnase gene, where the
ribonuclease barnase gene comprises at least one amber codon.
Optionally, the ribonuclease barnase gene can include two or more
amber codons.
[0047] In one embodiment, selecting or screening the pool of
(optionally mutant) tRNAs for members that are aminoacylated by an
introduced orthogonal RS(O-RS) can include: introducing a positive
selection or screening marker gene, wherein the positive marker
gene comprises a drug resistance gene (e.g., .beta.-lactamase gene,
comprising at least one of the selector codons, such as at least
one amber stop codon) or a gene essential to the organism, or a
gene that leads to detoxification of a toxic agent, along with the
O-RS, and the pool of (optionally mutant) tRNAs into a plurality of
cells from the second organism; and, identifying surviving or
screened cells grown in the presence of a selection or screening
agent, e.g., an antibiotic, thereby providing a pool of cells
possessing the at least one recombinant tRNA, where the at least
recombinant tRNA is aminoacylated by the O-RS and inserts an amino
acid into a translation product encoded by the positive marker
gene, in response to the at least one selector codons. In another
embodiment, the concentration of the selection and/or screening
agent is varied. Recombinant O-tRNAs produced by the methods of the
present invention are also included.
[0048] Methods for generating specific O-tRNA/O-RS pairs are
provided. Methods include: (a) generating a library of mutant tRNAs
derived from at least one tRNA from a first organism; (b)
negatively selecting or screening the library for (optionally
mutan) tRNAs that are aminoacylated by an aminoacyl-tRNA synthetase
(RS) from a second organism in the absence of a RS from the first
organism, thereby providing a pool of (optionally mutant) tRNAs;
(c) selecting or screening the pool of (optionally mutant) tRNAs
for members that are aminoacylated by an introduced orthogonal
RS(O-RS), thereby providing at least one recombinant O-tRNA. The at
least one recombinant O-tRNA recognizes a selector codon and is not
efficiency recognized by the RS from the second organism and is
preferentially aminoacylated by the O-RS. The method also includes
(d) generating a library of (optionally mutant) RSs derived from at
least one aminoacyl-tRNA synthetase (RS) from a third organism; (e)
selecting or screening the library of mutant RSs for members that
preferentially aminoacylate the at least one recombinant O-tRNA in
the presence of an unnatural amino acid and a natural amino acid,
thereby providing a pool of active (optionally mutant) RSs; and,
(f) negatively selecting or screening the pool for active
(optionally mutant) RSs that preferentially aminoacylate the at
least one recombinant O-tRNA in the absence of the unnatural amino
acid, thereby providing the at least one specific O-tRNA/O-RS pair,
wherein the at least one specific O-tRNA/O-RS pair comprises at
least one recombinant O-RS that is specific for the unnatural amino
acid and the at least one recombinant O-tRNA. Specific O-tRNA/O-RS
pairs produced by the methods are included. For example, the
specific O-tRNA/O-RS pair can include, e.g., a mutRNATyr-mutTyrRS
pair, such as a mutRNATyr-SS 12TyrRS pair, a mutRNALeu-mutLeuRS
pair, a mutRNAThr-mutThrRS pair, a mutRNAGlu-mutGluRS pair, or the
like. Additionally, such methods include wherein the first and
thrid organism are the same (e.g., Methanococcus jannaschii).
[0049] Methods for selecting an orthogonal tRNA-tRNA synthetase
pair for use in an in vivo translation system of a second organism
are also included in the present invention. The methods include:
introducing a marker gene, a tRNA and an aminoacyl-tRNA synthetase
(RS) isolated or derived from a first organism into a first set of
cells from the second organism; introducing the marker gene and the
tRNA into a duplicate cell set from a second organism; and,
selecting for surviving cells in the first set that fail to survive
in the duplicate cell set or screening for cells showing a specific
screening response that fail to give such response in the duplicate
cell set, wherein the first set and the duplicate cell set are
grown in the presence of a selection or screening agent, wherein
the surviving or screened cells comprise the orthogonal tRNA-tRNA
synthetase pair for use in the in the in vivo translation system of
the second organism. In one embodiment, comparing and selecting or
screening includes an in vivo complementation assay. The
concentration of the selection or screening agent can be
varied.
[0050] The organisms of the present invention comprise a variety of
organism and a variety of combinations. For example, the first and
the second organisms of the methods of the present invention can be
the same or different. In one embodiment, the organisms are
optionally a prokaryotic organism, e.g., Methanococcus jannaschii,
Methanobacterium thermoautotrophicum, Halobacterium, Escherichia
coli, A. fulgidus, P. furiosus, P. horikoshii, A. pernix, T
thermophilus, or the like. Alternatively, the organisms optionally
comprise a eukaryotic organism, e.g., plants (e.g., complex plants
such as monocots, or dicots), algae, protists, fungi (e.g., yeast,
etc), animals (e.g., mammals, insects, arthropods, etc.), or the
like. In another embodiment, the second organism is a prokaryotic
organism, e.g., Methanococcus jannaschii, Methanobacterium
thermoautotrophicum, Halobacterium, Escherichia coli, A. fulgidus,
Halobacterium, P. furiosus, P. horikoshii, A. pemix, T.
thermophilus, or the like. Alternatively, the second organism can
be a eukaryotic organism, e.g., a yeast, a animal cell, a plant
cell, a fungus, a mammalian cell, or the like. In various
embodiments the first and second organisms are different.
[0051] The various methods of the invention (above) optionally
comprise wherein selecting or screening comprises one or more
positive or negative selection or screening, e.g., a change in
amino acid permeability, a change in translation efficiency, and a
change in translational fidelity. Additionally, the one or more
change is optionally based upon a mutation in one or more gene in
an organism in which an orthogonal tRNA-tRNA synthetase pair are
used to produce such protein. Selecting and/or screening herein
optionally comprises wherein at least 2 selector codons within one
or more selection gene or within one or more screening gene are
use. Such multiple selector codons are optionally within the same
gene or within different screening/selection genes. Additionally,
the optional multiple selector codons are optionally different
selector codons or comprise the same type of selector codons.
[0052] Kits are an additional feature of the invention. For
example, the kits can include one or more translation system as
noted above (e.g., a cell), one or more unnatural amino acid, e.g.,
with appropriate packaging material, containers for holding the
components of the kit, instructional materials for practicing the
methods herein and/or the like. Similarly, products of the
translation systems (e.g., proteins such as EPO analogues
comprising unnatural amino acids) can be provided in kit form,
e.g., with containers for holding the components of the kit,
instructional materials for practicing the methods herein and/or
the like.
BRIEF DESCRIPTION OF THE DRAWINGS
[0053] FIG. 1 schematically illustrates site-specific incorporation
of unnatural amino acids into proteins in vivo. An orthogonal
aminoacyl-tRNA synthetase aminoacylates an orthogonal tRNA with an
unnatural amino acid. The acylated orthogonal tRNA inserts the
unnatural amino acid at the position specified by a selector codon,
e.g., a unique codon, which is introduced into the gene encoding a
protein of interest.
[0054] FIG. 2, Panel A and Panel B, schematically illustrates
examples of selection methods for active synthetases that
aminoacylate with unnatural amino acids. Panel A illustrates the
general selection/screen for aminoacyl-tRNA synthetases with
unnatural amino acids specificities. In the positive selection,
active synthetases with either natural or unnatural amino acid
specificities are identified; in the negative selection,
synthetases with natural amino acid specificities are eliminated.
Only synthetases charging the orthogonal tRNA with the unnatural
amino acid can survive both selections/screens. Panel B
schematically illustrates one embodiment of the selection/screen
for synthetases preferentially aminoacylating an O-tRNA with an
unnatural amino acid. For example, expression vectors containing an
orthogonal suppressor tRNA and a member of a library of mutated RS
with a positive selection marker, e.g., .beta.-lactamase, with a
selector codon, e.g., an amber codon, are introduced into an
organism and grown in the presence a selector agent, e.g.,
ampicillin. The expression of the positive selection marker allows
the cell to survive in the selection agent. Survivors encode
synthetases capable of charging any natural or unnatural amino acid
(aa) onto the O-tRNA. The active synthetases are transformed into a
second strain in the expression vector, and an expression vector
with a negative selection marker, e.g., a toxic gene, such as
barnase, that when expressed kills the cells, with one or more
selector codons, e.g., TAG. The cells are grown without the
unnatural amino acid. If the synthetase provided aminoacylates the
O-tRNA with a natural amino acid, the negative selection marker is
expressed and the cell dies. If the synthetase preferentially
aminoacylates the O-tRNA, no negative selection marker is
expressed, because there is no unnatural amino acid and the cell
lives. This provides at least one orthogonal synthetase that
preferentially aminoacylates the O-tRNA with the desired unnatural
codon.
[0055] FIG. 3 illustrates site-specific mutations to generate
directed libraries for tyrosine analogues.
[0056] FIG. 4 illustrates a consensus sequence for
pentafluorophenylalanin- e selection to generate directed libraries
for these analogues.
[0057] FIG. 5 schematically illustrates the transplantation of one
domain, e.g., the CPI domain, from one organism, e.g., Escherichia
coli, to the synthetase of other organism, e.g., Methanococcus
jannaschii TyrRS.
[0058] FIG. 6 schematically illustrates the construction of
chimeric Methanococcus jannaschii/Escherichia coli synthetases.
[0059] FIG. 7 schematically illustrates the generation of a library
of chimeric synthetases, e.g., Methanococcus jannaschii/Escherichia
coli synthetases.
[0060] FIG. 8 schematically illustrates an example for selection of
suppressor tRNAs that are poor substrates for an endogenous
synthetases, e.g., an Escherichia coli synthetase, and that are
charged efficiently by a cognate synthetase of interest. Expression
vectors that contain a member of a mutated tRNA library and another
vector with a negative selection marker, e.g., a toxic gene, such
as barnase, with one or more selector codons are introduced into a
cell of an organism. Survivors of the negative selection encode
mutated tRNAs that are either orthogonal to the organism or
non-functional. The vectors from the survivors are isolated and
transformed into other cells along with a positive selection
marker, e.g., .beta.-lactamase gene, with a selector codon. The
cells are grown in the presence of a selection agent, e.g.,
ampicillin, and an RS from an organism from the same source, e.g.,
Methanococcus jannaschii, as the tRNA. Survivors of this selection
encode mutant tRNA that are orthogonal to the cell's synthetases,
e.g., Escherichia coli's synthetases, and aminoacylated by RS from
the same source as the tRNA.
[0061] FIG. 9, Panel A and B, schematically illustrates a mutated
anticodon-loop tRNA library, Panel A, and a mutated all-loop
library, Panel B, from Methanococcus jannaschii tRNA.sub.TyrCUA.
Randomly mutated nucleotides (N) are shaded in black.
[0062] FIG. 10 schematically illustrates examples of structures of
unnatural base pairs which pair by forces other than hydrogen
bonding (PICS:PICS, 3MN:3MN, 7AI:7AI, Dipic:Py).
[0063] FIG. 11 is a graph of results of a negative selection method
for suppressor tRNAs, which shows the percentage of surviving cells
containing one of three constructs, for a given amount of time
based on the suppression of two amber codons in the barnase gene
introduced by a vector, e.g., plasmid pSCB2. This plasmid encodes
the barnase gene containing two amber codons. Selections are
carried out in GMML liquid medium, and 20 mM of arabinose is used
to induce barnase expression. Three constructs are indicated by the
following: (1) a circle which represents a control plasmid with no
suppressor tRNA; (2) a triangle which represents a suppressor tRNA
on plasmid, pAC-YYG1; and, (3) a square which represents a
suppressor tRNA on plasmid, pAC-JY.
[0064] FIG. 12 displays growth histograms, illustrating positive
selection based on the suppression of an amber codon in the
.beta.-lactamase gene. A vector encoding a suppressor tRNA, e.g.,
pAC plasmid, is cotransformed with a vector encoding a synthetase,
e.g., pBLAM-JYRS, in an organism, e.g., Escherichia coli DH10B
cells. The growth of cells harboring synthetase and different pAC
plasmids in liquid 2.times.YT medium with various concentrations of
ampicillin, e.g., 0, 100 and 500 .mu.g/ml, is shown in Panel A,
where pAC is a control plasmid with no suppressor tRNA, where
pAC-YYG1 is a plasmid with a suppressor tRNA, and where pAC-JY is a
plasmid with a suppressor tRNA. Panel B shows positive selection of
the same constructs using 2.times.YT agar plates with 500 .mu.g/ml
ampicillin. Three constructs are indicated by the following: (1) a
circle which represents a control plasmid with no suppressor tRNA;
(2) a triangle which represents a suppressor tRNA on plasmid,
pAC-YYG1; and, (3) a square which represents a suppressor tRNA on
plasmid, pAC-JY.
[0065] FIG. 13 illustrates DNA sequences of mutant suppressor tRNAs
selected from anticodon-loop and all-loop library. JY stands for
the wild-type Methanococcus jannaschii tRNACUATyrCUA.
[0066] FIG. 14 schematically illustrates a stereo view of the
active site of TyrRS. Residues from B. stearothermophilus TyrRS are
illustrated in the figure. Corresponding residues from
Methanococcus jannaschii TyrRS are Tyr.sup.32(Tyr.sup.34),
Glu.sup.107 (Asn.sup.123), Asp.sup.158(Asp.sup.176),
Ile.sup.159(Phe.sup.177), and Leu.sup.162(Leu.sup.180) with
residues from B. stearothermophilus TyrRS in parentheses.
[0067] FIG. 15 schematically illustrates a view of the active site
of TyrRS. Residues from B. stearothermophilus TyrRS are illustrated
in the figure. Corresponding residues from Methanococcus jannaschii
TyrRS are Tyr.sup.32(Tyr.sup.34), Asp.sup.158(Asp.sup.176),
Ile.sup.159(Phe.sup.177- ), Leu.sup.162(Leu.sup.180) and
Ala.sup.167(Gln.sup.189) with residues from B. stearothermophilus
TyrRS in parentheses.
[0068] FIG. 16, Panel A and Panel B schematically illustrate an
example of FACS-based selection and screening methods used to
generate a component of the present invention, e.g., orthogonal
synthetase. Panel A schematically illustrates vectors, e.g.,
plasmids, for expression of orthogonal synthetase library and
O-tRNA (library plasmid) and for the T7 RNA polymerase/GFP reporter
system (reporter plasmid), with one or more selector codons, e.g.,
TAG. Panel B schematically illustrates positive selection/negative
screen scheme, where the cells are grown the presence and absence
of the unnatural amino acid, the presence and absence of a
selection agent, and screened for fluorescing cells and
non-fluorescing cells in the screening process, where the "+" and
empty circles correspond to fluorescing and non-fluorescing cells,
respectively.
[0069] FIG. 17, Panel A, Panel B, Panel C and Panel D illustrates
an amplifiable fluorescence reporter system. Panel A schematically
illustrates vectors that can be used in the screen, e.g., plasmids,
such as pREP, where T7 RNA polymerase transcription is controlled
by the ara promoter; protein expression depends on suppression of
amber codons at varying locations in the gene. Reporter expression,
e.g., GFPuv expression is controlled by T7 RNA polymerase. The
reporter vector, e.g., plasmid pREP, is compatible for use with a
vector for expressing an orthogonal synthetase/tRNA pair, e.g., a
ColE1 plasmid. Panel B illustrates compositions and fluorescence
enhancement of T7 RNA polymerase gene constructs within pREP
(1-12). The construct number is indicated to the left of each.
Fluorescence enhancements, indicated to the right of each
construct, are calculated as the cell concentration-corrected ratio
of fluorescence, as measured fluorimetrically, of cells containing
pREP(1-12) and pQ or pQD. The position of the amber mutations
within a gene are indicated. Panel C illustrates cytometric
analysis of cells containing pREP (10) and either pQD (top) or pQ
(bottom). Panel D illustrates fluorimetric analyses of cells
containing pREP (10) and expressing various Escherichia coli
suppressor tRNAs. "None" indicates that the cells contain no
suppressor tRNA.
[0070] FIG. 18 schematically illustrates phage-based selection for
the incorporation of unnatural amino acids into a surface epitope.
For example, Escherichia coli carrying the mutant synthetase
library are infected by phage with a stop codon in a gene encoding
a surface protein. Phage containing an active synthetase display
the unnatural amino acid on the phage surface and are selected with
immobilized monoclonal antibodies.
[0071] FIG. 19 schematically illustrates an example of a molecule,
e.g., immobilized aminoalkyl adenylate analog of the aminoacyl
adenylate intermediate, used to screen displayed synthetases, e.g.,
phage-displayed synthetases, with unnatural amino acid
specificity.
[0072] FIG. 20 is a graph illustrating ampicillin resistance of
various orthogonal pairs from a variety of organisms. The figure
illustrates an example of finding an orthogonal pair using a
reporter constructs, each containing a reporter gene, e.g., a
.beta.-lactamase gene, with a selector codon, e.g., an amber codon,
and a suppressor tRNA (with a selector anticodon), where the
suppressor tRNA can be from a variety of organisms, e.g., A.
fulgidus, Halobacterium NRC-1, P. furiosus, P. horikoshii, and
Methanococcus jannaschii. The reporter constructs and cloned
synthetases from different organisms, e.g., M. thermoautotrophicum,
Methanococcus jannaschii, P. horikoshii, A. pernix, A. fulgidus,
Halobacterium NRC-1, and Escherichia coli are transformed into a
cell. Cells are grown in various concentrations of a selector
agent, e.g., ampicillin. Cells possessing an orthogonal tRNA/RS
pair are selected, e.g., using an in vivo complementation assay. As
shown, two systems showed suppression levels significant higher
than was observed with Escherichia coli synthetase. They are M.
thermoautotrophicum and Methanococcus jannaschii.
[0073] FIG. 21, Panel A and Panel B, illustrates mutated amber
suppressor tRNAs from a Halobacterium NRC-1, which are generated by
mutating, e.g., randomizing, the anticodon loop of the leucyl tRNA
and selecting (Panel B) for more efficient suppression of a
selector codon, e.g., an amber codon in a reporter gene(s), e.g.,
using a combination of selection steps, such as selection based on
.beta.-lactamase and selection based on barnase. Panel B
illustrates IC50 values in .mu.g/ml of ampicillin for a
.beta.-lactamase amber suppression system with three mutant tRNA
constructs, original amber mutant, optimized anticodon loop, and
optimized acceptor stem, alone or with an RS, e.g., MtLRS. The
optimized anticodon and optimized acceptor stem gave the highest
values in the .beta.-lactamase selection step.
[0074] FIG. 22 illustrates a tRNA suppressor for a base codon. The
tRNA suppressor illustrated in this figure was isolated from a
library derived from the Halobacterium NRC-1 TTG tRNA, where the
anticodon loop was randomized with 8 nucleotides and subjected to
ampicillin selection with a reporter construct containing a
lactamase gene with an AGGA codon at the A184 site.
[0075] FIG. 23 Panels A-D, illustrates the activity of the dominant
synthetase variant from each successful evolution experiment. FIG.
23A is a photograph illustrating long-wavelength ultraviolet
illumination of cells containing pREP/YC-JYCUA and the indicated
synthetase variant, grown in either the presence (+) or absence (-)
of the corresponding unnatural amino acid. FIG. 23B illustrates a
fluorimetric analysis of cells containing pREP/YC-JYCUA and the
indicated synthetase variant, grown in either the presence (left)
or absence (right) of the corresponding unnatural amino acid. FIG.
23C is a table that illustrates a Cm IC.sub.50 analysis of cells
containing pREP/YC-JYCUA and the indicated synthetase variant,
grown in either the presence or absence of the corresponding
unnatural amino acid. FIG. 23D illustrates a protein expression
analysis from cells containing pBAD/JYAMB4TAG and the indicated
synthetase variant, grown in either the presence (+) or absence (-)
of the corresponding unnatural amino acid.
[0076] FIG. 24, illustrates activity comparisons of OAY-RS variants
derived using a negative FACS-based screen (OAY-RS(1,3,5)) or
negative barnase-based selection (OAY-RS(B)). Cells containing
pREP/YC-JYCUA and the indicated synthetase variant were grown in
either the presence (solid block, left) or absence (solid block,
right) of the corresponding unnatural amino acid and analyzed
fluorimetrically. Fluorescence enhancement (bar, back) is
calculated as the cell concentration-corrected ratio of
fluorescence of cells grown in the presence versus the absence of
unnatural amino acid.
[0077] FIG. 25, Panels A-B, illustrate components of the
multipurpose reporter plasmid system for directing the evolution of
M. jannaschii TyrRS. FIG. 25A illustrates plasmid pREP/YC-JYCUA.
Plasmid pREP/YC-JYCUA is compatible for use with plasmid pBK and
variants. FIG. 25B illustrates structures of unnatural amino acids
used as targets for the evolution of M. jannaschii TyrRS.
[0078] FIG. 26 illustrates the strategy for the evolution of an
aminoacyl-tRNA synthetase using plasmid pREP/YC-JYCUA. Fluorescent
and non-fluorescent cells are shown in black and white,
respectively.
[0079] FIG. 27 illustrates a threonyl-tRNA synthetase from Thermus
thermophilus.
[0080] FIG. 28 illustrates the generation of an orthogonal tRNA for
a T. thermophilus orthogonal threonyl-tRNA/RS.
[0081] FIG. 29 illustrates exemplary unnatrual amino acids as
utilized in the current invention.
[0082] FIG. 30 illustrates exemplary unnatrual amino acids as
utilized in the current invention.
[0083] FIG. 31 illustrates exemplary unnatrual amino acids as
utilized in the current invention.
DETAILED DESCRIPTION
[0084] Introduction
[0085] Proteins are at the crossroads of virtually every biological
process, from photosynthesis and vision to signal transduction and
the immune response. These complex functions result from a
polyamide based polymer consisting of twenty relatively simple
building blocks arranged in a defined primary sequence.
[0086] The present invention includes methods and composition for
use in the site-specific incorporation of unnatural amino acids
directly into proteins in vivo. Importantly, the unnatural amino
acid is added to the genetic repertoire, rather than substituting
for one of the common 20 amino acids. The present invention
provides methods for generating, methods for identifying and
compositions comprising the components used by the biosynthetic
machinery to incorporate an unnatural amino acid into a protein.
The present invention, e.g., (i) allows the site-selective
insertion of one or more unnatural amino acids at any desired
position of any protein, (ii) is applicable to both prokaryotic and
eukaryotic cells, (iii) enables in vivo studies of mutant proteins
in addition to the generation of large quantities of purified
mutant proteins, and (iv) is adaptable to incorporate any of a
large variety of non-natural amino acids, into proteins in vivo.
Thus, in a specific polypeptide sequence a number of different
site-selective insertions of unnatural amino acids is possible.
Such insertions are optionally all of the same type (e.g., multiple
examples of one type of unnatural amino acid inserted at multiple
points in a polypeptide) or are optionally of diverse types (e.g.,
different unnatural amino acid types are inserted at multiple
points in a polypeptide).
[0087] Definitions
[0088] Before describing the present invention in detail, it is to
be understood that this invention is not limited to particular
compositions or biological systems, which can, of course, vary. It
is also to be understood that the terminology used herein is for
the purpose of describing particular embodiments only, and is not
intended to be limiting. As used in this specification and the
appended claims, the singular forms "a", "an" and "the" include
plural referents unless the content clearly dictates otherwise.
Thus, for example, reference to "a molecule" optionally includes
acombination of two or more such molecules, and the like.
[0089] Unless defined otherwise, all scientific and technical terms
are understood to have the same meaning as commonly used in the art
to which they pertain. For the purpose of the present invention,
the following terms are defined below.
[0090] As used herein, proteins and/or protein sequences are
"homologous" when they are derived, naturally or artificially, from
a common ancestral protein or protein sequence. Similarly, nucleic
acids and/or nucleic acid sequences are homologous when they are
derived, naturally or artificially, from a common ancestral nucleic
acid or nucleic acid sequence. For example, any naturally occurring
nucleic acid can be modified by any available mutagenesis method to
include one or more selector codon. When expressed, this
mutagenized nucleic acid encodes a polypeptide comprising one or
more unnatural amino acid. The mutation process can, of course,
additionally alter one or more standard codon, thereby changing one
or more standard amino acid in the resulting mutant protein as
well. Homology is generally inferred from sequence similarity
between two or more nucleic acids or proteins (or sequences
thereof). The precise percentage of similarity between sequences
that is useful in establishing homology varies with the nucleic
acid and protein at issue, but as little as 25% sequence similarity
is routinely used to establish homology. Higher levels of sequence
similarity, e.g., 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 99% or
more can also be used to establish homology. Methods for
determining sequence similarity percentages (e.g., BLASTP and
BLASTN using default parameters) are described herein and are
generally available.
[0091] The term "preferentially aminoacylates" refers to an
efficiency, e.g., about 70% efficient, about 75% efficient, about
85% efficient, about 90%, about 95%, about 99% or more efficient,
at which an O-RS aminoacylates an O-tRNA with an unnatural amino
acid compared to a naturally occurring tRNA or starting material
used to generate the O-tRNA. The unnatural amino acid is then
incorporated into a growing polypeptide chain with high fidelity,
e.g., at greater than about 75% efficiency for a given selector
codon, at greater than about 80% efficiency for a given selector
codon, at greater than about 90% efficiency for a given selector
codon, greater than about 95% efficiency for a given selector
codon, or greater than about 99% efficiency for a given selector
codon.
[0092] The term "selector codon" refers to codons recognized by the
O-tRNA in the translation process and not recognized by an
endogenous tRNA. The O-tRNA anticodon loop recognizes the selector
codon on the mRNA and incorporates its amino acid, e.g., an
unnatural amino acid, at this site in the polypeptide. Selector
codons can include, e.g., nonsense codons, such as, stop codons,
e.g., amber, ochre, and opal codons; four or more base codons;
codons derived from natural or unnatural base pairs and the like.
For a given system, a selector codon can also include one of the
natural three base codons, wherein the endogenous system does not
use said natural three base codon, e.g., a system that is lacking a
tRNA that recognizes the natural three base codon or a system
wherein the natural three base codon is a rare codon.
[0093] As used herein, the term "orthogonal" refers to a molecule
(e.g., an orthogonal tRNA (O-tRNA) and/or an orthogonal aminoacyl
tRNA synthetase (O-RS)) that is used with reduced efficiency by a
system of interest (e.g., a translational system, e.g., a cell).
Orthogonal refers to the inability or reduced efficiency, e.g.,
less than 20% efficient, less than 10% efficient, less than 5%
efficient, or e.g., less than 1% efficient, of an orthogonal tRNA
and/or orthogonal RS to function in the translation system of
interest. For example, an orthogonal tRNA in a translation system
of interest aminoacylates any endogenous RS of a translation system
of interest with reduced or even zero efficiency, when compared to
aminoacylation of an endogenous tRNA by the endogenous RS. In
another example, an orthogonal RS aminoacylates any endogenous tRNA
in the translation system of interest with reduced or even zero
efficiency, as compared to aminoacylation of the endogenous tRNA by
an endogenous RS. "Improvement in orthogonality" refers to enhanced
orthogonality compared to a starting material or a naturally
occurring tRNA or RS.
[0094] The term "complementary" refers to components of an
orthogonal pair, O-tRNA and O-RS that can function together, e.g.,
the O-RS aminoacylates the O-tRNA.
[0095] The term "derived from" refers to a component that is
isolated from an organism or isolated and modified, or generated,
e.g., chemically synthesized, using information of the component
from the organism.
[0096] The term "translation system" refers to the components
necessary to incorporate a naturally occurring amino acid into a
growing polypeptide chain (protein). For example, components can
include ribosomes, tRNAs, synthetases, mRNA and the like. The
components of the present invention can be added to a translation
system, in vivo or in vitro.
[0097] The term "inactive RS" refers to a synthetase that have been
mutated so that it no longer can aminoacylate its cognate tRNA with
an amino acid.
[0098] The term "selection agent" refers to an agent that when
present allows for a selection of certain components from a
population, e.g., an antibiotic, wavelength of light, an antibody,
a nutrient or the like. The selection agent can be varied, e.g.,
such as concentration, intensity, etc.
[0099] The term "positive selection marker" refers to a marker than
when present, e.g., expressed, activated or the like, results in
identification of an organism with the positive selection marker
from those without the positive selection marker.
[0100] The term "negative selection marker" refers to a marker than
when present, e.g., expressed, activated or the like, allows
identification of an organism that does not possess the desired
property (e.g., as compared to an organism which does possess the
desired property).
[0101] The term "reporter" refers to a component that can be used
to select components described in the present invention. For
example, a reporter can include a green fluorescent protein, a
firefly luciferase protein, or genes such as .beta.-gal/lacZ
(.beta.-galactosidase), Adh (alcohol dehydrogenase) or the
like.
[0102] The term "not efficiently recognized" refers to an
efficiency, e.g., less than about 10%, less than about 5%, or less
than about 1%, at which a RS from one organism aminoacylates
O-tRNA.
[0103] The term "eukaryote" refers to organisms belonging to the
phylogenetic domain Eucarya such as animals (e.g., mammals,
insects, reptiles, birds, etc.), ciliates, plants, fungi (e.g.,
yeasts, etc.), flagellates, microsporidia, protists, etc.
Additionally, the term "prokaryote" refers to non-eukaryotic
organisms belonging to the Eubacteria (e.g., Escherichia coli,
Thermus thermophilus, etc.) and Archaea (e.g., Methanococcus
jannaschii, Methanobacterium thermoautotrophicum, Halobacterium
such as Haloferax volcanii and Halobacterium species NRC-1, A.
fulgidus, P. furiosus, P. horikoshii, A. pernix, etc.) phylogenetic
domains
[0104] A "suppressor tRNA" is a tRNA that alters the reading of a
messenger RNA (mRNA) in a given translation system. A suppressor
tRNA can read through, e.g., a stop codon, a four base codon, or a
rare codon.
[0105] Discussion
[0106] The present invention relates to methods and compositions
for new components of biosynthetic translational machinery that
allows for the incorporation of unnatural amino acids into proteins
in vivo. Specifically, compositions comprising and methods for
generating orthogonal tRNAs and orthogonal-RS and orthogonal
tRNAs/orthogonal-RS pairs are provided. These components, when
introduced into a host cell, can be used in the translation system
of the cell to incorporate an unnatural amino acid in vivo into a
polypeptide (protein) of interest. For example, this can provide
site-specific unnatural amino acid mutagenesis; or, optionally,
random unnatural amino acid mutagenesis. The orthogonal tRNA
delivers the unnatural amino acid in response to a selector codon
and the orthogonal synthetase preferentially aminoacylates an
orthogonal tRNA with the unnatural amino acid. The O-RS does not
efficiently aminoacylate the orthogonal tRNA with any of the common
twenty amino acids. Methods for making and identifying orthogonal
pairs are also provided.
[0107] The site-specific incorporation of unnatural amino acids
into proteins in vivo is schematically illustrated in FIG. 1. A
selector codon, e.g., a unique codon, is introduced into a gene of
interest. The gene is transcribed into mRNA and conventional
translation begins on the ribosome. Endogenous synthetases
aminoacylate endogenous tRNAs with natural amino acids (aa) in the
presence of ATP. An orthogonal tRNA is enzymatically aminoacylated
by an orthogonal synthetase with an unnatural amino acid in the
presence of ATP. When the ribosome encounters a selector codon, an
orthogonal tRNA, which is modified to contain a selector anticodon,
e.g., a unique anticodon, it is able to decode the mutation as an
unnatural amino acid, and translation proceeds to the full-length
product with the incorporated unnatural amino acid.
[0108] Orthogonal Aminoacyl tRNA Synthetase, O-RS
[0109] In order to specifically incorporate an unnatural amino acid
in vivo, the substrate specificity of the synthetase is altered so
that only the desired unnatural amino acid, but not any common 20
amino acids are charged to the tRNA. If the orthogonal synthetase
is promiscuous, it will result in mutant proteins with a mixture of
natural and unnatural amino acids at the target position. For
instance, in an attempt to site-specifically, incorporate p-F-Phe,
a yeast amber suppressor tRNAPheCUA/phenylalanyl-tRNA synthetase
pair was used in a p-F-Phe resistant, Phe auxotrophic Escherichia
coli strain. See, e.g., R. Furter, Protein Sci., 7:419 (1998).
Because yeast PheRS does not have high substrate specificity for
p-F-Phe, the mutagenesis site was translated with 64-75% p-F-Phe
and the remainder as Phe and Lys even in the excess of p-F-Phe
added to the growth media. In addition, at the Phe codon positions,
7% p-F-Phe was found, indicating that the endogenous Escherichia
coli PheRS incorporates p-F-Phe in addition to Phe. Because of its
translational infidelity, this approach is not generally applicable
to other unnatural amino acids. Modification of the substrate
specificity of a synthetase was expected to be difficult due to the
high intrinsic fidelity of the natural synthetases and the fact
that unnatural amino acids are not required for any cellular
function. The present invention solves this problem and provides
composition of, and methods for, generating synthetases that have
modified substrate specificity, such as an unnatural amino acid.
Using the components of the present invention, the efficiency of
incorporation of an unnatural amino acid into is, e.g., greater
than about 75%, greater than about 85%, greater than about 95%,
greater than about 99% or more.
[0110] Compositions of the present invention include an orthogonal
aminoacyl-tRNA synthetase (O-RS), where the O-RS preferentially
aminoacylates an orthogonal tRNA (O-tRNA) with an unnatural amino
acid, optionally, in vivo. In one embodiment, the O-RS comprises a
nucleic acid comprising a polynucleotide sequence selected from the
group consisting of: SEQ ID NO: 4-34 (see, Table 5) and a
complementary polynucleotide sequence thereof. In another
embodiment, the O-RS has improved or enhanced enzymatic properties,
e.g., the K.sub.m is lower, the k.sub.cat is higher, the value of
k.sub.cat/K.sub.m is higher or the like, for the unnatural amino
acid compared to a naturally occurring amino acid, e.g., one of the
20 known amino acids. Sequences of exemplary O-tRNA and O-RS
molecules can be found in Example 10.
[0111] Methods for producing an O-RS are based on generating a pool
of mutant synthetases from the framework of a wild-type synthetase,
and then selecting for mutated RSs based on their specificity for
an unnatural amino acid relative to the common twenty. To isolate
such a synthetase, the selection methods of the present invention
are: (i) sensitive, as the activity of desired synthetases from the
initial rounds can be low and the population small; (ii) "tunable",
since it is desirable to vary the selection stringency at different
selection rounds; and, (iii) general, so that it can be used for
different unnatural amino acids.
[0112] The present invention provides methods to generate an
orthogonal aminoacyl tRNA synthetase by mutating the synthetase,
e.g., at the active site in the synthetase, at the editing
mechanism site in the synthetase, at different sites by combining
different domains of synthetases, or the like, and applying a
selection process. FIG. 2, Panel A schematically illustrates an in
vivo selection/screen strategy, which is based on the combination
of a positive selection followed by a negative selection. In the
positive selection, suppression of the selector codon introduced at
a nonessential position(s) of a positive marker allows cells to
survive under positive selection pressure. In the presence of both
natural and unnatural amino acids, survivors thus encode active
synthetases charging the orthogonal suppressor tRNA with either a
natural or unnatural amino acid. In the negative selection,
suppression of a selector codon introduced at a nonessential
position(s) of a negative marker removes synthetases with natural
amino acid specificities. Survivors of the negative and positive
selection encode synthetases that aminoacylate (charge) the
orthogonal suppressor tRNA with unnatural amino acids only. These
synthetases can then be subjected to further mutagenesis, e.g., DNA
shuffling or other recursive mutagenesis methods. Of course, in
other embodiments, the invention optionall cn utilize different
orders of steps to identify (e.g., O-RS, O-tRNA, pairs, etc.),
e.t., negative selection/screening followed by positive
selection/screening or vice verse or any such combinations
thereof.
[0113] For example, see, FIG. 2, Panel B. In FIG. 2, Panel B, a
selector codon, e.g., an amber codon, is placed in a reporter gene,
e.g., an antibiotic resistance gene, such as .beta.-lactamase, with
a selector codon, e.g., TAG. This is placed in an expression vector
with members of the mutated RS library. This expression vector
along with an expression vector with an orthogonal tRNA, e.g., a
orthogonal suppressor tRNA, are introduced into a cell, which is
grown in the presence of a selection agent, e.g., antibiotic media,
such as ampicillin. Only if the synthetase is capable of
aminoacylating (charging) the suppressor tRNA with some amino acid
does the selector codon get decoded allowing survival of the cell
on antibiotic media.
[0114] Applying this selection in the presence of the unnatural
amino acid, the synthetase genes that encode synthetases that have
some ability to aminoacylate are selected away from those
synthetases that have no activity. The resulting pool of
synthetases can be charging any of the 20 naturally occurring amino
acids or the unnatural amino acid. To further select for those
synthetases that exclusively charge the unnatural amino acid, a
second selection, e.g., a negative selection, is applied. In this
case, an expression vector containing a negative selection marker
and an O-tRNA is used, along with an expression vector containing a
member of the mutated RS library. This negative selection marker
contains at least one selector codon, e.g., TAG. These expression
vectors are introduced into another cell and grown without
unnatural amino acids and, optionally, a selection agent, e.g.,
tetracycline. In the negative selection, those synthetases with
specificities for natural amino acids charge the orthogonal tRNA,
resulting in suppression of a selector codon in the negative marker
and cell death. Since no unnatural amino acid is added, synthetases
with specificities for the unnatural amino acid survive. For
example, a selector codon, e.g., a stop codon, is introduced into
the reporter gene, e.g., a gene that encodes a toxic protein, such
as barnase. If the synthetase is able to charge the suppressor tRNA
in the absence of unnatural amino acid, the cell will be killed by
translating the toxic gene product. Survivors passing both
selection/screens encode synthetases specifically charging the
orthogonal tRNA with an unnatural amino acid.
[0115] In one embodiment, methods for producing at least one
recombinant orthogonal aminoacyl-tRNA synthetase (O-RS) include:
(a) generating a library of mutant RSs derived from at least one
aminoacyl-tRNA synthetase (RS) from a first organism; (b) selecting
the library of mutant RSs for members that aminoacylate an
orthogonal tRNA (O-tRNA) in the presence of an unnatural amino acid
and a natural amino acid, thereby providing a pool of active mutant
RSs; and, (c) negatively selecting the pool for active mutant RSs
that preferentially aminoacylate the O-tRNA in the absence of the
unnatural amino acid, thereby providing the at least one
recombinant O-RS; wherein the at least one recombinant O-RS
preferentially aminoacylates the O-tRNA with the unnatural amino
acid. Optionally, more mutations are introduced by mutagenesis,
e.g., random mutagenesis, recombination or the like, into the
selected synthetase genes to generate a second-generation
synthetase library, which is used for further rounds of selection
until a mutant synthetase with desired activity is evolved.
Recombinant O-RSs produced by the methods are included in the
present invention. As explained below, orthogonal tRNA/synthetase
pairs or the invention are also optionally generated by importing
such from a first organism into a second organism.
[0116] In one embodiment, the RS is an inactive RS. The inactive RS
can be generated by mutating an active RS. For example, the
inactive RS can be generated by mutating at least about 5 amino
acids to different amino acids, e.g., alanine.
[0117] The library of mutant RSs can be generated using various
mutagenesis techniques known in the art. For example, the mutant
RSs can be generated by site-specific mutations, random point
mutations, in vitro homologous recombinant, chimeric constructs or
the like. In one embodiment, mutations are introduced into the
editing site of the synthetase to hamper the editing mechanism
and/or to alter substrate specificity. See, e.g., FIG. 3 and FIG.
4. FIG. 3 illustrates site-specific mutations to generate directed
libraries for tyrosine analogues. FIG. 4 illustrates a consensus
sequence for pentafluorophenylalanine selection to generate
directed libraries for these analogues. Libraries of mutant RSs
also include chimeric synthetase libraries, e.g., libraries of
chimeric Methanococcus jannaschii/Escherichia coli synthetases. The
domain of one synthetase can be added or exchanged with a domain
from another synthetase. FIG. 5 schematically illustrates the
transplantation of one domain, e.g., the CPI domain, from one
organism, e.g., Escherichia coli, to the synthetase of other
organism, e.g., Methanococcus jannaschii TyrRS. CPI can be
transplanted from Escherichia coli TyrRS to H. sapiens TyrRS. See,
e.g., Wakasugi, K., et al., EMBO J. 17:297-305 (1998). FIG. 6
schematically illustrates the construction of chimeric
Methanococcus jannaschii/Escherichia coli synthetases and FIG. 7
schematically illustrates the generation of a library of chimeric
synthetases, e.g., Methanococcus jannaschii/Escherichia coli
synthetases. See, e.g., Sieber, et al., Nature Biotechnology,
19:456-460 (2001). The chimeric library is screened for a variety
of properties, e.g., for members that are expressed and in frame,
for members that lack activity with a desired synthetase, and/or
for members that show activity with a desired synthetase.
[0118] In one embodiment, the positive selection step includes:
introducing a positive selection marker, e.g., an antibiotic
resistance gene, or the like, and the library of mutant RSs into a
plurality of cells, wherein the positive selection marker comprises
at least one selector codon, e.g., an amber codon; growing the
plurality of cells in the presence of a selection agent; selecting
cells that survive in the presence of the selection agent by
suppressing the at least one selector codon in the positive
selection marker, thereby providing a subset of positively selected
cells that contains the pool of active mutant RSs. Optionally, the
selection agent concentration can be varied.
[0119] In one embodiment, negative selection includes: introducing
a negative selection marker with the pool of active mutant RSs from
the positive selection into a plurality of cells of a second
organism, wherein the negative selection marker is an antibiotic
resistance gene, e.g., a chloramphenicol acetyltransferase (CAT)
gene, comprising at least one selector codon; and, selecting cells
that survive in a 1st media supplemented with the unnatural amino
acid and a selection agent, but fail to survive in a 2nd media not
supplemented with the unnatural amino acid and the selection agent,
thereby providing surviving cells with the at least one recombinant
O-RS. Optionally, the concentration of the selection agent is
varied.
[0120] The 1.sup.st and 2.sup.nd media described above can include,
e.g., a direct replica plate method. For example, after passing the
positive selection, cells are grown in the presence of either
ampicillin or chloramphenicol and the absence of the unnatural
amino acid. Those cells that do not survive are isolated from a
replica plate supplemented with the unnatural amino acid. No
transformation into a second negative selection strain is needed,
and the phenotype is known. Compared to other potential selection
markers, a positive selection based on antibiotic resistance offers
the ability to tune selection stringency by varying the
concentration of the antibiotic, and to compare the suppression
efficiency by monitoring the highest antibiotic concentration cells
can survive. In addition, the growth process is also an enrichment
procedure. This can lead to a quick accumulation of the desired
phenotype.
[0121] In another embodiment, negatively selecting the pool for
active mutant RSs includes: isolating the pool of active mutant RSs
from the positive selection step (b); introducing a negative
selection marker, wherein the negative selection marker is a toxic
marker gene, e.g., a ribonuclease barnase gene, comprising at least
one selector codon, and the pool of active mutant RSs into a
plurality of cells of a second organism; and selecting cells that
survive in a 1st media not supplemented with the unnatural amino
acid, but fail to survive in a 2nd media supplemented with the
unnatural amino acid, thereby providing surviving cells with the at
least one recombinant O-RS, wherein the at least one recombinant
O-RS is specific for the unnatural amino acid. Optionally, the
negative selection marker comprises two or more selector
codons.
[0122] In one aspect, positive selection is based on suppression of
a selector codon in a positive selection marker, e.g., a
chloramphenicol acetyltransferase (CAT) gene comprising a selector
codon, e.g., an amber stop codon, in the CAT gene, so that
chloramphenicol can be applied as the positive selection pressure.
In addition, the CAT gene can be used as both a positive marker and
negative marker as describe herein in the presence and absence of
unnatural amino acid. Optionally, the CAT gene comprising a
selector codon is used for the positive selection and a negative
selection marker, e.g., a toxic marker, such as a barnase gene
comprising at least one or more selector codons, is used for the
negative selection.
[0123] In another aspect, positive selection is based on
suppression of a selector codon at nonessential position in the
.beta.-lactamase gene, rendering cells ampicillin resistant; and a
negative selection using the ribonuclease barnase as the negative
marker is used. In contrast to .beta.-lactamase, which is secreted
into the periplasm, CAT localizes in the cytoplasm; moreover,
ampicillin is bacteriocidal, while chloramphenicol is
bacteriostatic.
[0124] The recombinant O-RS can be further mutated and selected. In
one embodiment, the methods for producing at least one recombinant
orthogonal aminoacyl-tRNA synthetase (O-RS) can further comprise:
(d) isolating the at least one recombinant O-RS; (e) generating a
second set of mutated O-RS derived from the at least one
recombinant O-RS; and, (f) repeating steps (b) and (c) until a
mutated O-RS is obtained that comprises an ability to
preferentially aminoacylate the O-tRNA. Optionally, steps (d)-(f)
are repeated, e.g., at least about two times. In one aspect, the
second set of mutated O-RS can be generated by mutagenesis, e.g.,
random mutagenesis, site-specific mutagenesis, recombination or a
combination thereof.
[0125] The stringency of the selection steps, e.g., the positive
selection step (b), the negative selection step (c) or both the
positive and negative selection steps (b) and (c), in the above
described-methods, optionally include varying the selection
stringency. For example, because barnase is an extremely toxic
protein, the stringency of the negative selection can be controlled
by introducing different numbers of selector codons into the
barnase gene. In one aspect of the present invention, the
stringency is varied because the desired activity can be low during
early rounds. Thus, less stringent selection criteria are applied
in early rounds and more stringent criteria are applied in later
rounds of selection.
[0126] Other types of selections can be used in the present
invention for, e.g., O-RS, O-tRNA, and O-tRNA/O-RS pair. For
example, the positive selection step (b), the negative selection
step (c) or both the positive and negative selection steps (b) and
(c) can include using a reporter, wherein the reporter is detected
by fluorescence-activated cell sorting (FACS). For example, a
positive selection can be done first with a positive selection
marker, e.g., chloramphenicol acetyltransferase (CAT) gene, where
the CAT gene comprises a selector codon, e.g., an amber stop codon,
in the CAT gene, which followed by a negative selection screen,
that is based on the inability to suppress a selector codon(s),
e.g., two or more, at positions within a negative marker, e.g., T7
RNA polymerase gene. In one embodiment, the positive selection
marker and the negative selection marker can be found on the same
vector, e.g., plasmid. Expression of the negative marker drives
expression of the reporter, e.g., green fluorescent protein (GFP).
The stringency of the selection and screen can be varied, e.g., the
intensity of the light need to fluorescence the reporter can be
varied. In another embodiment, a positive selection can be done
with a reporter as a positive selection marker, which is screened
by FACs, followed by a negative selection screen, that is based on
the inability to suppress a selector codon(s), e.g., two or more,
at positions within a negative marker, e.g., barnase gene.
[0127] Optionally, the reporter is displayed on a cell surface,
e.g., on a phage display or the like. Cell-surface display, e.g.,
the OmpA-based cell-surface display system, relies on the
expression of a particular epitope, e.g., a poliovirus C3 peptide
fused to an outer membrane porin OmpA, on the surface of the
Escherichia coli cell. The epitope is displayed on the cell surface
only when a selector codon in the protein message is suppressed
during translation. The displayed peptide then contains the amino
acid recognized by one of the mutant aminoacyl-tRNA synthetases in
the library, and the cell containing the corresponding synthetase
gene can be isolated with antibodies raised against peptides
containing specific unnatural amino acids. The OmpA-based
cell-surface display system was developed and optimized by Georgiou
et al. as an alternative to phage display. See, Francisco, J. A.,
Campbell, R., Iverson, B. L. & Georgoiu, G. Production and
fluorescence-activated cell sorting of Escherichia coli expressing
a functional antibody fragment on the external surface. Proc. Natl.
Acad. Sci. USA 90:10444-8 (1993).
[0128] Other embodiments of the present invention include carrying
one or more of the selection steps in vitro. The selected
component, e.g., synthetase and/or tRNA, can then be introduced
into a cell for use in in vivo incorporation of an unnatural amino
acid.
[0129] Orthogonal tRNA
[0130] Compositions of an orthogonal tRNA (O-tRNA) are also a
feature of the invention, e.g., where the O-tRNA recognizes a
selector codon and the O-tRNA is preferentially aminoacylated with
an unnatural amino acid by an orthogonal aminoacyl-tRNA synthetase.
In one embodiment, the O-tRNA comprises a nucleic acid comprising a
polynucleotide sequence selected from the group consisting of: SEQ
ID NO: 4-34 (see, Table 5) and a complementary polynucleotide
sequence thereof.
[0131] Methods for producing a recombinant orthogonal tRNA (O-tRNA)
are provided herein. For example, to improve the orthogonality of a
tRNA while preserving its affinity toward a desired RS, the methods
include a combination of negative and positive selections with a
mutant suppressor tRNA library in the absence and presence of the
cognate synthetase, respectively. See, FIG. 8. In the negative
selection, a selector codon(s) is introduced in a marker gene,
e.g., a toxic gene, such as barnase, at a nonessential position.
When a member of the mutated tRNA library, e.g., derived from
Methanococcus jannaschii, is aminoacylated by endogenous host,
e.g., Escherichia coli synthetases (i.e., it is not orthogonal to
the host, e.g., Escherichia coli synthetases), the selector codon,
e.g., an amber codon, is suppressed and the toxic gene product
produced leads to cell death. Cells harboring orthogonal tRNAs or
non-functional tRNAs survive. Survivors are then subjected to a
positive selection in which a selector codon, e.g., an amber codon,
is placed in a positive marker gene, e.g., a drug resistance gene,
such a lactamase gene. These cells also contain an expression
vector with a cognate RS. These cells are grown in the presence of
a selection agent, e.g., ampicillin. tRNAs are then selected for
their ability to be aminoacylated by the coexpressed cognate
synthetase and to insert an amino acid in response to this selector
codon. Cells harboring non-functional tRNAs, or tRNAs that cannot
be recognized by the synthetase of interest are sensitive to the
antibiotic. Therefore, tRNAs that: (i) are not substrates for
endogenous host, e.g., Escherichia coli, synthetases; (ii) can be
aminoacylated by the synthetase of interest; and (iii) are
functional in translation survive both selections.
[0132] Methods of producing a recombinant O-tRNA include: (a)
generating a library of mutant tRNAs derived from at least one
tRNA, e.g., a suppressor tRNA, from a first organism; (b)
negatively selecting the library for mutant tRNAs that are
aminoacylated by an aminoacyl-tRNA synthetase (RS) from a second
organism in the absence of a RS from the first organism, thereby
providing a pool of mutant tRNAs; and, (c) selecting the pool of
mutant tRNAs for members that are aminoacylated by an introduced
orthogonal RS(O-RS), thereby providing at least one recombinant
O-tRNA; wherein the at least one recombinant O-tRNA recognizes a
selector codon and is not efficiency recognized by the RS from the
second organism and is preferentially aminoacylated by the O-RS. In
one embodiment, the recombinant O-tRNA possesses an improvement of
orthogonality.
[0133] Libraries of mutated tRNA are constructed. See, for example,
FIG. 9. Mutations can be introduced at a specific position(s),
e.g., at a nonconservative position(s), or at a conservative
position, at a randomized position(s), or a combination of both in
a desired loop of a tRNA, e.g., an anticodon loop, (D arm, V loop,
T.psi.C arm) or a combination of loops or all loops. Chimeric
libraries of tRNA are also included in the present invention. It
should be noted that libraries of tRNA synthetases from various
organism (e.g., microorganisms such as eubacteria or
archaebacteria) such as libraries comprising natural diversity
(such as libraries that comprise natural diversity (see, e.g., U.S.
Pat. No. 6,238,884 to Short et al. and references therein, U.S.
Pat. No. 5,756,316 to Schallenberger et al; U.S. Pat. No. 5,783,431
to Petersen et al; U.S. Pat. No. 5,824,485 to Thompson et al; and
U.S. Pat. No. 5,958,672 to Short et al), are optionally constructed
and screened for orthogonal pairs.
[0134] In one embodiment, negatively selecting the library for
mutant tRNAs that are aminoacylated by an aminoacyl-tRNA synthetase
(step (b) above) includes: introducing a toxic marker gene, wherein
the toxic marker gene comprises at least one of the selector codons
and the library of mutant tRNAs into a plurality of cells from the
second organism; and, selecting surviving cells, wherein the
surviving cells contain the pool of mutant tRNAs comprising at
least one orthogonal tRNA or nonfunctional tRNA. For example, the
toxic marker gene is optionally a ribonuclease barnase gene,
wherein the ribonuclease barnase gene comprises at least one amber
codon. Optionally, the ribonuclease barnase gene can include two or
more amber codons. The surviving cells can be selected, e.g., by
using a comparison ratio cell density assay.
[0135] In one embodiment, selecting the pool of mutant tRNAs for
members that are aminoacylated by an introduced orthogonal RS(O-RS)
can include: introducing a positive selection marker gene, wherein
the positive selection marker gene comprises a drug resistance
gene, e.g., a .beta.-lactamase gene, comprising at least one of the
selector codons, e.g., a .beta.-lactamase gene comprising at least
one amber stop codon, the O-RS, and the pool of mutant tRNAs into a
plurality of cells from the second organism; and, selecting
surviving cells grown in the presence of a selection agent, e.g.,
an antibiotic, thereby providing a pool of cells possessing the at
least one recombinant tRNA, wherein the recombinant tRNA is
aminoacylated by the O-RS and inserts an amino acid into a
translation product encoded by the positive marker gene, in
response to the at least one selector codons. In another
embodiment, the concentration of the selection agent is varied.
Recombinant O-tRNAs produced by the methods are included in the
present invention.
[0136] As described above for generating O-RS, the stringency of
the selection steps can be varied. In addition, other
selection/screening procedures, which are described herein, such as
FACs, cell and phage display can also be used.
[0137] Selector Codons
[0138] Selector codons of the present invention expand the genetic
codon framework of protein biosynthetic machinery. For example, a
selector codon includes, e.g., a unique three base codon, a
nonsense codon, such as a stop codon, e.g., an amber codon, or an
opal codon, an unnatural codon, a four (or more) base codon or the
like. A number of selector codons can be introduced into a desired
gene, e.g., one or more, two or more, more than three, etc.
Additionally, it will be appreciated that multiple different (or
similar or identical) unnatural amino acids can thus be
incorporated precisely into amino acids (i.e., thruough use of the
multiple selector codons).
[0139] The 64 genetic codons code for 20 amino acids and 3 stop
codons. Because only one stop codon is needed for translational
termination, the other two can in principle be used to encode
nonproteinogenic amino acids. The amber stop codon, UAG, has been
successfully used in in vitro biosynthetic system and in Xenopus
oocytes to direct the incorporation of unnatural amino acids. Among
the 3 stop codons, UAG is the least used stop codon in Escherichia
coli. Some Escherichia coli strains contain natural suppressor
tRNAs, which recognize UAG and insert a natural amino acid in
response to UAG. In addition, these amber suppressor tRNAs have
been widely used in conventional protein mutagenesis. Different
species preferentially use different codons for their natural amino
acids, such preferentiallity is optionally utilized in
designing/choosing the selector codons herein.
[0140] Although discussed with reference to unnatural amino acids
herein, it will be appreciated that a similar strategy can be used
incorporate a natural amino acid in response to a particular
selector codon. That is, a synthetase can be modified to load a
natural amino acid onto an orthogonal tRNA that recognizes a
selector codon in a manner similar to the loading of an unnatural
amino acid as described throughout.
[0141] In one embodiment, the methods involve the use of a selector
codon that is a stop codon for the incorporation of unnatural amino
acids in vivo. For example, an O-tRNA is generated that recognizes
the stop codon, e.g., UAG, and is aminoacylated by an O-RS with a
desired unnatural amino acid. This O-tRNA is not recognized by the
naturally occurring aminoacyl-tRNA synthetases. Conventional
site-directed mutagenesis can be used to introduce the stop codon,
e.g., TAG, at the site of interest in the protein gene. See, e.g.,
Sayers, J. R., Schmidt, W. Eckstein, F. 5', 3' Exonuclease in
phosphorothioate-based oligonucleotide-directed mutagenesis.
Nucleic Acids Res, 791-802 (1988). When the O-RS, O-tRNA and the
mutant gene are combined in vivo, the unnatural amino acid is
incorporated in response to the UAG codon to give a protein
containing the unnatural amino acid at the specified position.
[0142] The incorporation of unnatural amino acids in vivo can be
done without significant perturbation of the host, e.g.,
Escherichia coli. For example, because the suppression efficiency
for the UAG codon depends upon the competition between the O-tRNA,
e.g., the amber suppressor tRNA, and the release factor 1 (RF1)
(which binds to the UAG codon and initiates release of the growing
peptide from the ribosome), the suppression efficiency can be
modulated by, e.g., either increasing the expression level of
O-tRNA, e.g., the suppressor tRNA, or using an RF1 deficient
strain. Additionally, suppression efficiency and unnatural amino
acid uptake by carrying out random mutagenesis on an organism or on
a portion of an organism's genome and performing proper selection
using, e.g., one of the reporter systems described herein.
[0143] Unnatural amino acids can also be encoded with rare codons.
For example, when the arginine concentration in an in vitro protein
synthesis reaction is reduced, the rare arginine codon, AGG, has
proven to be efficient for insertion of Ala by a synthetic tRNA
acylated with alanine. See, e.g., C. H. Ma, W. Kudlicki, O. W.
Odom, G. Kramer and B. Hardesty, Biochemistry, 32:7939 (1993). In
this case, the synthetic tRNA competes with the naturally occurring
tRNA.sup.Arg, which exists as a minor species in Escherichia coli.
Some organisms do not use all triplet codons. An unassigned codon
AGA in Micrococcus luteus has been utilized for insertion of amino
acids in an in vitro transcription/translation extract. See, e.g.,
A. K. Kowal and J. S. Oliver, Nucl. Acid. Res., 25:4685 (1997).
Components of the present invention can be generated to use these
rare codons in vivo.
[0144] Selector codons also comprise four or more base codons, such
as, four, five six or more. Examples of four base codons include,
e.g., AGGA, CUAG, UAGA, CCCU and the like. Examples of five base
codons include, e.g., AGGAC, CCCCU, CCCUC, CUAGA, CUACU, UAGGC and
the like. For example, in the presence of mutated O-tRNAs, e.g., a
special frameshift suppressor tRNAs, with anticodon loops, e.g.,
with at least 8-10 nt anticodon loops, the four or more base codon
is read as single amino acid. In other embodiments, the anticodon
loops can decode, e.g., at least a four-base codon, at least a
five-base codon, or at least a six-base codon or more. Since there
are 256 possible four-base codons, multiple unnatural amino acids
can be encoded in the same cell using the four or more base codon.
See also, J. Christopher Anderson et al., Exploring the Limits of
Codon and Anticodon Size, Chemistry and Biology, Vol. 9, 237-244
(2002); Thomas J. Magliery, Expanding the Genetic Code: Selection
of Efficient Suppressors of Four-base Codons and Identification of
"Shifty" Four-base Codons with a Library Approach in Escherichia
coli, J. Mol. Biol. 307: 755-769 (2001).
[0145] Methods of the present invention include using extended
codons based on frameshift suppression. Four or more base codons
can insert, e.g., one or multiple unnatural amino acids into the
same protein. For example, four-base codons have been used to
incorporate unnatural amino acids into proteins using in vitro
biosynthetic methods. See, e.g., C. H. Ma, W. Kudlicki, O. W. Odom,
G. Kramer and B. Hardesty, Biochemistry, 1993, 32, 7939 (1993);
and, T. Hohsaka, D. Kajihara, Y. Ashizuka, H. Murakami and M.
Sisido, J. Am. Chem. Soc., 121:34 (1999). CGGG and AGGU were used
to simultaneously incorporate 2-naphthylalanine and an NBD
derivative of lysine into streptavidin in vitro with two chemically
acylated frameshift suppressor tRNAs. See, e.g., T. Hohsaka, Y.
Ashizuka, H. Sasaki, H. Murakami and M. Sisido, J. Am. Chem. Soc.,
121:12194 (1999). In an in vivo study, Moore et al. examined the
ability of tRNALeu derivatives with NCUA anticodons to suppress
UAGN codons (N can be U, A, G, or C), and found that the quadruplet
UAGA can be decoded by a tRNALeu with a UCUA anticodon with ai
efficiency of 13 to 26% with little decoding in the 0 or -1 frame.
See, B. Moore, B. C. Persson, C. C. Nelson, R. F. Gesteland and J.
F. Atkins, J. Mol. Biol., 298:195 (2000). In one embodiment,
extended codons based on rare codons or nonsense codons can be used
in present invention, which can reduce missense readthrough and
frameshift suppression at unwanted sites.
[0146] A translational bypassing system can also be used to
incorporate an unnatural amino acid in a desired polypeptide. In a
translational bypassing system, a large sequence is inserted into a
gene but is not translated into protein. The sequence contains a
structure that serves as a cue to induce the ribosome to hop over
the sequence and resume translation downstream of the
insertion.
[0147] Alternatively, or in combination with others methods
described above to incorporate an unnatural amino acid in a
polypeptide, a trans-translation system can be used. This system
involves a molecule called tmRNA present in Escherichia coli. This
RNA molecule is structurally related to an alanyl tRNA and is
aminoacylated by the alanyl synthetase. The difference between
tmRNA and tRNA is that the anticodon loop is replaced with a
special large sequence. This sequence allows the ribosome to resume
translation on sequences that have stalled using an open reading
frame encoded within the tmRNA as template. In the present
invention, an orthogonal tmRNA can be generated that is
preferentially aminoacylated with an orthogonal synthetase and
loaded with an unnatural amino acid. By transcribing a gene by the
system, the ribosome stalls at a specific site; the unnatural amino
acid is introduced at that site, and translation resumes using the
sequence encoded within the orthogonal tmRNA.
[0148] Selector codons also optionally include unnatural base
pairs. These unnatural base pairs further expand the existing
genetic alphabet. One extra base pair increases the number of
triplet codons from 64 to 125. Properties of third base pairs
include stable and selective base pairing, efficient enzymatic
incorporation into DNA with high fidelity by a polymerase, and the
efficient continued primer extension after synthesis of the nascent
unnatural base pair. Descriptions of unnatural base pairs which can
be adapted for methods and compositions include, e.g., Hirao, et
al., An unnatural base pair for incorporating amino acid analogues
into protein, Nature Biotechnology, 20:177-182 (2002). Other
publications are listed below.
[0149] For in vivo usage, the unnatural nucleoside is membrane
permeable and is phosphorylated to form the corresponding
triphosphate. In addition, the increased genetic information is
stable and not destroyed by cellular enzymes. Previous efforts by
Benner and others took advantage of hydrogen bonding patterns that
are different from those in canonical Watson-Crick pairs, the most
noteworthy example of which is the iso-C:iso-G pair. See, e.g., C.
Switzer, S. E. Moroney and S. A. Benner, J. Am. Chem. Soc.,
111:8322 (1989); and, J. A. Piccirilli, T. Krauch, S. E. Moroney
and S. A. Benner, Nature, 1990, 343:33 (1990); and E. T. Kool,
Curr. Opin. Chem. Biol., 4:602 (2000). These bases in general
mispair to some degree with natural bases and cannot be
enzymatically replicated. Kool and co-workers demonstrated that
hydrophobic packing interactions between bases can replace hydrogen
bonding to drive the formation of base pair. See, E. T. Kool, Curr.
Opin. Chem. Biol., 4:602 (2000); and, K. M. Guckian and E. T. Kool,
Angew. Chem. Int. Ed. Engl., 36, 2825 (1998). In an effort to
develop an unnatural base pair satisfying all the above
requirements, Schultz, Romesberg and co-workers have systematically
synthesized and studied a series of unnatural hydrophobic bases.
The PICS:PICS self-pair, which is shown in FIG. 10, is found to be
more stable than natural base pairs, and can be efficiently
incorporated into DNA by the Klenow fragment of Escherichia coli
DNA polymerase I (KF). See, e.g., D. L. McMinn, A. K. Ogawa, Y. Q.
Wu, J. Q. Liu, P. G. Schultz and F. E. Romesberg, J. Am. Chem.
Soc., 121:11586 (1999); and, A. K. Ogawa, Y. Q. Wu, D. L. McMinn,
J. Q. Lu, P. G. Schultz and F. E. Romesberg, J. Am. Chem. Soc.,
122:3274 (2000). A 3MN:3MN self-pair can be synthesized by KF with
efficiency and selectivity sufficient for biological function. See,
e.g., A. K. Ogawa, Y. Q. Wu, M. Berger, P. G. Schultz and F. E.
Romesberg, J. Am. Chem. Soc., 122:8803 (2000). However, both bases
act as a chain terminator for further replication. A mutant DNA
polymerase has been recently evolved that can be used to replicate
the PICS self pair. In addition, a 7AI self pair can be replicated
using a combination of KF and pol .beta. polymerase. See, e.g., E.
J. L. Tae, Y. Q. Wu, G. Xia, P. G. Schultz and F. E. Romesberg, J.
Am. Chem. Soc., 123:7439 (2001). A novel metallobase pair,
Dipic:Py, has also been developed, which forms a stable pair upon
binding Cu(II). See, E. Meggers, P. L. Holland, W. B. Tolman, F. E.
Romesberg and P. G. Schultz, J. Am. Chem. Soc., 122:10714 (2000).
Because extended codons and unnatural codons are intrinsically
orthogonal to natural codons, the methods of the present invention
can take advantage of this property to generate orthogonal tRNAs
for them.
[0150] Orthogonal tRNA and Orthogonal Aminoacyl-tRNA Synthetase
Pairs
[0151] An orthogonal pair is composed of an O-tRNA, e.g., a
suppressor tRNA, a frameshift tRNA, or the like, and an O-RS. The
O-tRNA is not acylated by endogenous synthetases and is capable of
decoding a selector codon, as described above. The O-RS recognizes
the O-tRNA, e.g., with an extended anticodon loop, and
preferentially aminoacylates the O-tRNA with an unnatural amino
acid. Methods for generating orthogonal pairs along with
compositions of orthogonal pairs are included in the present
invention. The development of multiple orthogonal tRNA/synthetase
pairs can allow the simultaneous incorporation of multiple
unnatural amino acids using different codons into the same
polypeptide/protein.
[0152] In the present invention, methods and related compositions
relate to the generation of orthogonal pairs (O-tRNA/O-RS) that can
incorporate an unnatural amino acid into a protein in vivo. For
example, compositions of O-tRNAs of the present invention can
comprise an orthogonal aminoacyl-tRNA synthetase (O-RS). In one
embodiment, the O-tRNA and the O-RS can be complementary, e.g., an
orthogonal O-tRNA/O-RS pair. Examples of pairs include a
mutRNATyr-mutTyrRS pair, such as a mutRNATyr-SS12TyrRS pair, a
mutRNALeu-mutLeuRS pair, a mutRNAThr-mutThrRS pair, a
mutRNAGlu-mutGluRS pair, or the like. In one embodiment, an
orthogonal pair of the present invention comprises the desired
properties of the orthogonal tRNA-aminoacyl-tRNA synthetase pair
and is other than a mutRNAGln-mutGlnRS derived from Escherichia
coli, a mutRNAAsp-mutAspRS derived from yeast or a
mutRNAPheCUA-mutphenlalanineRS from yeast, where these pairs do not
possess the properties of the pairs of the present invention.
[0153] The O-tRNA and the O-RS can be derived by mutation of a
naturally occurring tRNA and/or RS from a variety of organisms,
which are described under sources and hosts. In one embodiment, the
O-tRNA and O-RS are derived from at least one organism. In another
embodiment, the O-tRNA is derived by mutation of a naturally
occurring or mutated naturally occurring tRNA from a first organism
and the O-RS is derived by mutation of a naturally occurring or
mutated naturally occurring RS from a second organism.
[0154] Methods for generating specific O-tRNA/O-RS pairs are also
provided in the present invention. These methods solve the problems
discussed below for the other strategies that were attempted to
generate orthogonal tRNA/RS pairs. Specifically, methods of the
present invention include: (a) generating a library of mutant tRNAs
derived from at least one tRNA from a first organism; (b)
negatively selecting the library for mutant tRNAs that are
aminoacylated by an aminoacyl-tRNA synthetase (RS) from a second
organism in the absence of a RS from the first organism, thereby
providing a pool of mutant tRNAs; (c) selecting the pool of mutant
tRNAs for members that are aminoacylated by an introduced
orthogonal RS(O-RS), thereby providing at least one recombinant
O-tRNA. The at least one recombinant O-tRNA recognizes a selector
codon and is not efficiency recognized by the RS from the second
organism and is preferentially aminoacylated by the O-RS. The
method also includes: (d) generating a library of mutant RSs
derived from at least one aminoacyl-tRNA synthetase (RS) from a
third organism; (e) selecting the library of mutant RSs for members
that preferentially aminoacylate the at least one recombinant
O-tRNA in the presence of an unnatural amino acid and a natural
amino acid, thereby providing a pool of active mutant RSs; and, (f)
negatively selecting the pool for active mutant RSs that
preferentially aminoacylate the at least one recombinant O-tRNA in
the absence of the unnatural amino acid, thereby providing the at
least one specific O-tRNA/O-RS pair, where the at least one
specific O-tRNA/O-RS pair comprises at least one recombinant O-RS
that is specific for the unnatural amino acid and the at least one
recombinant O-tRNA. Pairs produced by the methods of the present
invention are also included.
[0155] Previously, generation of an orthogonal tRNA/synthetase pair
from an existing Escherichia coli tRNA/synthetase pair was
attempted. The method involves eliminating the tRNA's affinity
toward its cognate synthetase by mutating nucleotides at the
tRNA-synthetase interface while preserving its orthogonality to
other synthetases and its ability to function in translation. Using
the cognate wild-type synthetase as the starting template, a mutant
synthetase is then evolved that uniquely recognizes the engineered
orthogonal tRNA. Based on an analysis of the X-ray crystal
structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS)
complexed with tRNAGln2, three sites ("knobs") in tRNAGln2 were
identified which make specific contacts with GlnRS. See, e.g., D.
R. Liu, T. J. Magliery and P. G. Schultz, Chem. Biol., 4:685
(1997); and, D. R. Liu, T. J. Magliery, M. Pastmak and P. G.
Schultz, Proc. Natl. Acad. Sci. USA, 94:10092 (1997). These sites
were mutated in the tRNA, and mutant suppressor tRNAs containing
all possible combinations of knobs 1, 2, and 3 were generated and
tested individually by in vitro aminoacylation with GlnRS and in
vitro suppression of amber mutants of chorismate mutase. A mutant
tRNA (O-tRNA) bearing all three-knob mutations was shown to be
orthogonal to all endogenous Escherichia coli synthetases and
competent in translation. Next, multiple rounds of DNA shuffling
together with oligonucleotide-directed mutagenesis were used to
generate libraries of mutant GlnRS's. These mutant enzymes were
selected for their ability to acylate the O-tRNA in vivo using
Escherichia coli strain BT235. Only if a mutant GlnRS charges the
O-tRNA with glutamine can the genomic amber codon in lacZ be
suppressed, enabling BT235 cells to grow on lactose minimal media.
Several mutant synthetases surviving each round of selection were
purified and assayed in vitro. The ratio of wild-type (wt) tRNAGln
acylation to O-tRNA acylation by mutant synthetase decreased
significantly upon multiple rounds of selection. However, no mutant
Escherichia coli GlnRS's have been evolved that charge the O-tRNA
more efficiently than wild-type Escherichia coli tRNAGln2. The best
mutant evolved after seven rounds of DNA shuffling and selection
acylates the O-tRNA at only one-ninth the rate of wt tRNAGln.
However, these experiments failed to produce a synthetase candidate
with the desired properties, e.g., a synthetase that does not
acylate any wt tRNA, since misacylation of a wt tRNA with an
unnatural amino acid could result in a lethal phenotype. In
addition, the mutations within the tRNA interact in complicated,
non-additive ways with respect to both aminoacylation and
translation. See, D. R. Liu, T. J. Magliery and P. G. Schultz,
Chem. Biol., 14:685 (1997). Thus, alternative methods are typically
used to provide a functional pair with the desired properties.
[0156] A second strategy for generating an orthogonal
tRNA/synthetase pair involves importing a tRNA/synthetase pair from
another organism into Escherichia coli. The properties of the
heterologous synthetase candidate include, e.g., that it does not
charge any Escherichia coli tRNA, and the properties of the
heterologous tRNA candidate include, e.g., that it is not acylated
by any Escherichia coli synthetase. In addition, the suppressor
tRNA derived from the heterologous tRNA is orthogonal to all
Escherichia coli synthetases. Schimmel et al. reported that
Escherichia coli GlnRS (EcGlnRS) does not acylate Saccharomyces
cerevisiae tRNAGln (EcGlnRS lacks an N-terminal RNA-binding domain
possessed by Saccharomyces cerevisiae GlnRS (ScGlnRS)). See, E. F.
Whelihan and P. Schimmel, EMBO J., 16:2968 (1997). The
Saccharomyces cerevisiae amber suppressor tRNAGln (SctRNAGlnCUA)
was then analyzed to determine whether it is also not a substrate
for EcGlnRS. In vitro aminoacylation assays showed this to be the
case; and in vitro suppression studies show that the SctRNAGlnCUA
is competent in translation. See, e.g., D. R. Lu and P. G. Schultz,
Proc. Natl. Acad. Sci. USA, 96:4780 (1999). It was further shown
that ScGlnRS does not acylate any Escherichia coli tRNA, only the
SctRNAGlnCUA in vitro. The degree to which ScGlnRS is able to
aminoacylate the SctRNAGlnCUA in Escherichia coli was also
evaluated using an in vivo complementation assay. An amber nonsense
mutation was introduced at a permissive site in the
.beta.-lactamase gene. Suppression of the mutation by an amber
suppressor tRNA should produce full-length .beta.-lactamase and
confer ampicillin resistance to the cell. When only SctRNAGlnCUA is
expressed, cells exhibit an IC.sub.50 of 20 .mu.g/mL ampicillin,
indicating virtually no acylation by endogenous Escherichia coli
synthetases; when SctRNAGlnCUA is coexpressed with ScGlnRS, cells
acquire an IC.sub.50 of about 500 .mu.g/mL ampicillin,
demonstrating that ScGlnRS acylates SctRNAGlnCUA efficiently in
Escherichia coli. See, D. R. Liu and P. G. Schultz, Proc. Natl.
Acad. Sci. USA, 96:4780 (1999). The Saccharomyces cerevisiae
tRNAGlnCUA/GlnRS is orthogonal to Escherichia coli.
[0157] This strategy was later applied to a tRNA.sup.AsP/AspRS
system. Saccharomyces cerevisiae tRNAAsP is known to be orthogonal
to Escherichia coli synthetases. See, e.g., B. P. Doctor and J. A.
Mudd, J. Biol. Chem., 238:3677 (1963); and, Y. Kwok and J. T. Wong,
Can. J. Biochem., 58:213 (1980). It was demonstrated that an amber
suppressor tRNA derived from it (SctRNAAspCUA) is also orthogonal
in Escherichia coli using the in vivo .beta.-lactamase assay
described above. However, the anticodon of tRNA.sup.Asp is a
critical recognition element of AspRS, see, e.g., R. Giege, C.
Florentz, D. Kern, J. Gangloff, G. Eriani and D. Moras, Biochimie,
78:605 (1996), and mutation of the anticodon to CUA results in a
loss of affinity of the suppressor for AspRS. An Escherichia coli
AspRS E93K mutant has been shown to recognize Escherichia coli
amber suppressor tRNAAspCUA about an order of magnitude better than
wt AspRS. See, e.g., F. Martin, `Thesis`, Universite Louis Pasteur,
Strasbourg, France, 1995. It was speculated that introduction of
the related mutation in Saccharomyces cerevisiae AspRS (E188K)
might restore its affinity for SctRNAAspCUA. It was determined that
the Saccharomyces cerevisiae AspRS(E188K) mutant does not acylate
Escherichia coli tRNAs, but charges SctRNAAspCUA with moderate
efficiency as shown by in vitro aminoacylation experiments. See,
e.g., M. Pastrnak, T. J. Magliery and P. G. Schultz, Helv. Chim.
Acta, 83:2277 (2000). Although the SctRNAAspCUA/ScAspRS(E188K- )
can serve as another orthogonal pair in Escherichia coli, it
possesses weak activity.
[0158] A similar approach involves the use of a heterologous
synthetase as the orthogonal synthetase but a mutant initiator tRNA
of the same organism or a related organism as the orthogonal tRNA.
RajBhandary and coworkers found that an amber mutant of human
initiator tRNAfMet is acylated by Escherichia coli GlnRS and acts
as an amber suppressor in yeast cells only when EcGlnRS is
coexpressed. See, A. K. Kowal, C. Kohrer and U. L. RajBhandary,
Proc. Natl. Acad. Sci. USA. 98:2268 (2001). This pair thus
represents an orthogonal pair for use in yeast. Also, an
Escherichia coli initiator tRNAfMet amber mutant was found that is
inactive toward any Escherichia coli synthetases. A mutant yeast
TyrRS was selected that charges this mutant tRNA, resulting in an
orthogonal pair in Escherichia coli. See, A. K. Kowal, et al,
(2001), supra.
[0159] The prokaryotic and eukaryotic tRNATyr/TyrRS pairs have
significant differences: the identity elements of prokaryotic
tRNATyr include a long variable arm in contrast to the short arm of
eukaryotic tRNATyr. In addition, eukaryotic tRNATyr contains a
C.sub.1:G72 positive recognition element whereas prokaryotic
tRNATyr has no such consensus base pair. In vitro studies have also
shown that tRNATyr of Saccharomyces cerevisiae and H. sapiens
cannot be aminoacylated by bacterial synthetases, nor do their
TyrRS aminoacylate bacterial tRNA. See, e.g., K. Wakasugi, C. L.
Quinn, N. Tao and P. Schimmel, EMBO J., 17:297 (1998); and, T. A.
Kleeman, D. Wei, K. L. Simpson and E. A. First. J. Biol. Chem.,
272:14420 (1997). But, in spite of all these promising features for
orthogonality, in vivo .beta.-lactamase complementation assays
showed that the amber suppressor tRNATyrCUA derived from both
Saccharomyces cerevisiae and H. sapiens are not orthogonal in
Escherichia coli. See, e.g., L. Wang, T. J. Magliery, D. R. Liu and
P. G. Schultz, J. Am. Chem. Soc., 122:5010 (2000). The
susceptibility of the suppressor tRNA to acylation by Escherichia
coli synthetases is due to the change of one single nucleotide in
the anticodon (G34 to C34).
[0160] Using the methods of the present invention, the pairs and
components of pairs desired above are evolved to generate
orthogonal tRNA/synthetase pairs that possess desired
characteristic, e.g., that can preferentially aminoacylate an
O-tRNA with an unnatural amino acid.
[0161] Source and Host Organisms
[0162] The orthogonal tRNA-RS pair, e.g., derived from at least a
first organism or at least two organisms, which can be the same or
different, can be used in a variety of organisms, e.g., a second
organism. The first and the second organisms of the methods of the
present invention can be the same or different. In one embodiment,
the first organism is a prokaryotic organism, e.g., Methanococcus
jannaschii, Methanobacterium thernoautotrophicum, Halobacterium,
Escherichia coli, A. fulgidus, Halobacterium, P. furiosus, P.
horikoshii, A. pernix, T. thermophilus, or the like. Alternatively,
the first organism is a eukaryotic organism, e.g., plants (e.g.,
complex plants such as monocots, or dicots), algae, protists, fungi
(e.g., yeast, etc), animals (e.g., mammals, insects, arthropods,
etc.), or the like. In another embodiment, the second organism is a
prokaryotic organism, Methanococcus jannaschii, Methanobacterium
thermoautotrophicum, Halobacterium; Escherichia coli, A. fulgidus,
Halobacterium, P. furiosus, P. horikoshii, A. pernix, T.
thermophilus, or the like. Alternatively, the second organism can
be a eukaryotic organism, e.g., plants, fungi, animals, or the
like.
[0163] As described above, the individual components of a pair can
be derived from the same organism or different organisms. For
example, tRNA can be derived from a prokaryotic organism, e.g., an
archaebacterium, such as Methanococcus jannaschii and Halobacterium
NRC-1 or a eubacterium, such as Escherichia coli, while the
synthetase can be derived from same or another prokaryotic
organism, such as, Methanococcus jannaschii, Archaeoglobus
fulgidus, Methanobacterium thermoautotrophicum, P. furiosus, P.
horikoshii, A. pernix, T. thermophilus, Halobacterium, Escherichia
coli or the like. Eukaryotic sources can also be used, e.g., plants
(e.g., complex plants such as monocots, or dicots), algae,
protists, fungi (e.g., yeast, etc.), animals (e.g., mammals,
insects, arthropods, etc.), or the like.
[0164] Methods for selecting an orthogonal tRNA-tRNA synthetase
pair for use in an in vivo translation system of a second organism
are also included in the present invention. The methods include:
introducing a marker gene, a tRNA and an aminoacyl-tRNA synthetase
(RS) isolated or derived from a first organism into a first set of
cells from the second organism; introducing the marker gene and the
tRNA into a duplicate cell set from the second organism; and,
selecting for surviving cells in the first set that fail to survive
in the duplicate cell set, where the first set and the duplicate
cell set are grown in the presence of a selection agent, and where
the surviving cells comprise the orthogonal tRNA-tRNA synthetase
pair for use in the in the in vivo translation system of the second
organism. In one embodiment, comparing and selecting includes an in
vivo complementation assay. In another embodiment, the
concentration of the selection agent is varied.
[0165] For example, a tRNA/synthetase pair can be chosen based on
where the identity elements, which are recognition sites of the
tRNA for the synthetase, are found. For example, a tRNA/synthetase
pair is chosen when the identity elements are outside of the
anticodon, e.g., the tRNATyr/TyrRS pair from the archaebacterial
Methanococcus jannaschii. This TyrRS is missing most of the
non-conserved domain binding for the anticodon loop of its tRNATyr,
but can discriminate tRNA with C1:G72 from that with G1:C72.
Furthermore, the Methanococcus jannaschii TyrRS(MjTyrRS)
aminoacylates Saccharomyces cerevisiae but not Escherichia coli
crude tRNA. See, e.g., B. A. Steer and P. Schimmel, J. Biol. Chem.,
274:35601 (1999). Using an in vivo complementation assay with an
expression vector containing a reporter gene, e.g.,
.beta.-lactamase gene, with at least one selector codon, cells
expressing the Methanococcus jannaschii tRNATyrCUA (Mj tRNATyrCUA)
alone survive to an IC.sub.50 of 55 .mu.g/mL ampicillin; cells
coexpressing Mj tRNATyrCUA with its TyrRS survive to an IC.sub.50
of 1220 ug/mL ampicillin. Although Mj tRNATyrCUA is less orthogonal
in Escherichia coli than the SctRNAGlnCUA (IC.sub.50 20 .mu.g/mL),
the MjTyrRS has higher aminoacylation activity toward its cognate
amber suppressor tRNA. See, e.g., L. Wang, T. J. Magliery, D. R.
Liu and P. G. Schultz, J. Am. Chem. Soc., 122:5010 (2000). As a
result, Methanococcus jannaschii/TyrRS is identified as an
orthogonal pair in Escherichia coli and can be selected for use in
an in vivo translation system.
[0166] Unnatural Amino Acids
[0167] A wide variety of unnatural amino acids can be used in the
methods of the invention. The unnatural amino acid can be chosen
based on desired characteristics of the unnatural amino acid, e.g.,
function of the unnatural amino acid, such as modifying protein
biological properties such as toxicity, biodistribution, or half
life, structural properties, spectroscopic properties, chemical
and/or photochemical properties, catalytic properties, ability to
react with other molecules (either covalently or noncovalently), or
the like.
[0168] As used herein an "unnatural amino acid" refers to any amino
acid, modified amino acid, or amino acid analogue other than
selenocysteine and the following twenty genetically encoded
alpha-amino acids: alanine, arginine, asparagine, aspartic acid,
cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine,
leucine, lysine, methionine, phenylalanine, proline, serine,
threonine, tryptophan, tyrosine, valine. The generic structure of
an alpha-amino acid is illustrated by Formula I: 1
[0169] An unnatural amino acid is typically any structure having
Formula I wherein the R group is any substituent other than one
used in the twenty natural amino acids. See, e.g., any biochemistry
text such as Biochemistry by L. Stryer, 3.sup.rd ed. 1988, Freeman
and Company, New York, for structures of the twenty natural amino
acids. Note that, the unnatural amino acids of the present
invention may be naturally occurring compounds other than the
twenty alpha-amino acids above. Because the unnatural amino acids
of the invention typically differ from the natural amino acids in
side chain only, the unnatural amino acids form amide bonds with
other amino acids, e.g., natural or unnatural, in the same manner
in which they are formed in naturally occurring proteins. However,
the unnatural amino acids have side chain groups that distinguish
them from the natural amino acids. For example, R in Formula I
optionally comprises an alkyl-, aryl-, acyl-, keto-, azido-,
hydroxyl-, hydrazine, cyano-, halo-, hydrazide, alkenyl, alkynl,
ether, thiol, seleno-, sulfonyl-, borate, boronate, phospho,
phosphono, phosphine, heterocyclic, enone, imine, aldehyde, ester,
thioacid, hydroxylamine, amino group, or the like or any
combination thereof. Other unnatural amino acids of interest
include, but are not limited to, amino acids comprising a
photoactivatable cross-linker, spin-labeled amino acids,
fluorescent amino acids, metal binding amino acids,
metal-containing amino acids, radioactive amino acids, amino acids
with novel functional groups, amino acids that covalently or
noncovalently interact with other molecules, photocaged and/or
photoisomerizable amino acids, amino acids comprising biotin or a
biotin analogue, glycosylated amino acids such as a sugar
substituted serine, other carbohydrate modified amino acids, keto
containing amino acids, amino acids comprising polyethylene glycol
or polyether, heavy atom substituted amino acids, chemically
cleavable and/or photocleavable amino acids, amino acids with an
elongated side chains as compared to natural amino acids, e.g.,
polyethers or long chain hydrocarbons, e.g., greater than about 5
or greater than about 10 carbons, carbon-linked sugar-containing
amino acids, redox-active amino acids, amino thioacid containing
amino acids, and amino acids comprising one or more toxic
moiety.
[0170] In addition to unnatural amino acids that contain novel side
chains, unnatural amino acids also optionally comprise modified
backbone structures, e.g., as illustrated by the structures of
Formula II and III: 2
[0171] wherein Z typically comprises OH, NH.sub.2, SH, NH--R', or
S--R'; X and Y, which may be the same or different, typically
comprise S or O, and R and R', which are optionally the same or
different, are typically selected from the same list of
constituents for the R group described above for the unnatural
amino acids having Formula I as well as hydrogen. For example,
unnatural amino acids of the invention optionally comprise
substitutions in the amino or carboxyl group as illustrated by
Formulas II and III. Unnatural amino acids of this type include,
but are not limited to, .alpha.-hydroxy acids, .alpha.-thioacids
.alpha.-aminothiocarboxylates, e.g., with side chains corresponding
to the common twenty natural amino acids or unnatural side chains.
In addition, substitutions at the .alpha.-carbon optionally include
L, D, or .alpha.-.alpha.-disubstituted amino acids such as
D-glutamate, D-alanine, D-methyl-O-tyrosine, aminobutyric acid, and
the like. Other structural alternatives include cyclic amino acids,
such as proline analogues as well as 3, 4, 6, 7, 8, and 9 membered
ring proline analogues, .beta. and .gamma. amino acids such as
substituted .beta.-alanine and .gamma.-amino butyric acid.
[0172] For example, many unnatural amino acids are based on natural
amino acids, such as tyrosine, glutamine, phenylalanine, and the
like. Tyrosine analogs include para-substituted tyrosines,
ortho-substituted tyrosines, and meta substituted tyrosines,
wherein the substituted tyrosine comprises an acetyl group, a
benzoyl group, an amino group, a hydrazine, an hydroxyamine, a
thiol group, a carboxy group, an isopropyl group, a methyl group, a
C.sub.6-C.sub.20 straight chain or branched hydrocarbon, a
saturated or unsaturated hydrocarbon, an O-methyl group, a
polyether group, a nitro group, or the like. In addition, multiply
substituted aryl rings are also contemplated. Glutamine analogs of
the invention include, but are not limited to, .alpha.-hydroxy
derivatives, .gamma.-substituted derivatives, cyclic derivatives,
and amide substituted glutamine derivatives. Example phenylalanine
analogs include, but are not limited to, meta-substituted
phenylalanines, wherein the substituent comprises a hydroxy group,
a methoxy group, a methyl group, an allyl group, an acetyl group,
or the like. Specific examples of unnatural amino acids include,
but are not limited to, O-methyl-L-tyrosine, an
L-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, an
O-4-allyl-L-tyrosine, a 4-propyl-L-tytosine, a
tri-O-acetyl-GlcNAc.beta.-serine, an L-Dopa, a fluorinated
phenylalanine, an isopropyl-L-phenylalanine, a
p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a
p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a
phosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine,
a p-amino-L-phenylalanine, and an isopropyl-L-phenylalanine, and
the like. The structures of a variety of non-limiting unnatural
amino acids are provided in the figures, e.g., FIGS. 29, 30, and
31.
[0173] Typically, the unnatural amino acids of the invention are
selected or designed to provide additional characteristics
unavailable in the twenty natural amino acids. For example,
unnatural amino acid are optionally designed or selected to modify
the biological properties of a protein, e.g., into which they are
incorporated. For example, the following properties are optionally
modified by inclusion of an unnatural amino acid into a protein:
toxicity, biodistribution, solubility, stability, e.g., thermal,
hydrolytic, oxidative, resistance to enzymatic degradation, and the
like, facility of purification and processing, structural
properties, spectroscopic properties, chemical and/or photochemical
properties, catalytic activity, redox potential, half-life, ability
to react with other molecules, e.g., covalently or noncovalently,
and the like.
[0174] Further details regarding unnatural amino acids are
described in corresponding application, "In vivo Incorporation of
Unnatural Amino Acids", attorney docket number 54-000120PC/US,
filed Apr. 19, 2002, which is incorporated herein by reference.
[0175] Use of Mutant tRNA and O-RS and O-tRNA/O-RS Pairs
[0176] The compositions of the present invention and compositions
made by the methods of the present invention optionally are in a
cell. The O-tRNA/O-RS pairs or individual components of the present
invention can then be used in a host system's translation
machinery, which results in an unnatural amino acid being
incorporated into a protein. The corresponding patent application
"In vivo Incorporation of Unnatural Amino Acids", attorney docket
number 54-000120PC/US by Schultz, et al. describes this process and
is incorporated herein by reference. For example, when an
O-tRNA/O-RS pair is introduced into a host, e.g., Escherichia coli,
the pair leads to the in vivo incorporation of an unnatural amino
acid, e.g., a synthetic amino acid, such as O-methyl-L-tyrosine,
which can be exogenously added to the growth medium, into a
protein, e.g., dihydrofolate reductase or a therapeutic protein
such as EPO, in response to a selector codon, e.g., an amber
nonsense codon. Optionally, the compositions of the present
invention can be in an in vitro translation system, or in an in
vivo system(s).
[0177] Nucleic Acid and Polypeptide Sequence Variants
[0178] As described above and below, the invention provides for
nucleic acid polynucleotide sequences and polypeptide amino acid
sequences, e.g., O-tRNAs and O-RSs, and, e.g., compositions and
methods comprising said sequences. Examples of said sequences,
e.g., O-tRNAs and O-RSs are disclosed herein. However, one of skill
in the art will appreciate that the invention is not limited to
those sequences disclosed herein. One of skill will appreciate that
the present invention also provides many related and unrelated
sequences with the functions described herein, e.g., encoding an
O-tRNA or an O-RS.
[0179] One of skill will also appreciate that many variants of the
disclosed sequences are included in the invention. For example,
conservative variations of the disclosed sequences that yield a
functionally identical sequence are included in the invention.
Variants of the nucleic acid polynucleotide sequences, wherein the
variants hybridize to at least one disclosed sequence, are
considered to be included in the invention. Unique subsequences of
the sequences disclosed herein, as determined by, e.g., standard
sequence comparison techniques, are also included in the
invention.
[0180] Conservative Variations
[0181] Owing to the degeneracy of the genetic code, "silent
substitutions" (i.e., substitutions in a nucleic acid sequence
which do not result in an alteration in an encoded polypeptide) are
an implied feature of every nucleic acid sequence which encodes an
amino acid. Similarly, "conservative amino acid substitutions," in
one or a few amino acids in an amino acid sequence are substituted
with different amino acids with highly similar properties, are also
readily identified as being highly similar to a disclosed
construct. Such conservative variations of each disclosed sequence
are a feature of the present invention.
[0182] "Conservative variations" of a particular nucleic acid
sequence refers to those nucleic acids which encode identical or
essentially identical amino acid sequences, or, where the nucleic
acid does not encode an amino acid sequence, to essentially
identical sequences, see, Table 1 below. One of skill will
recognize that individual substitutions, deletions or additions
which alter, add or delete a single amino acid or a small
percentage of amino acids (typically less than 5%, more typically
less than 4%, 2% or 1%) in an encoded sequence are "conservatively
modified variations" where the alterations result in the deletion
of an amino acid, addition of an amino acid, or substitution of an
amino acid with a chemically similar amino acid. Thus,
"conservative variations" of a listed polypeptide sequence of the
present invention include substitutions of a small percentage,
typically less than 5%, more typically less than 2% or 1%, of the
amino acids of the polypeptide sequence, with a conservatively
selected amino acid of the same conservative substitution group.
Finally, the addition of sequences which do not alter the encoded
activity of a nucleic acid molecule, such as the addition of a
non-functional sequence, is a conservative variation of the basic
nucleic acid.
1TABLE 1 Conservative Substitution Groups 1 Alanine (A) Serine (S)
Threonine (T) 2 Aspartic acid (D) Glutamic acid (E) 3 Asparagine
(N) Glutamine (Q) 4 Arginine (R) Lysine (K) 5 Isoleucine (I)
Leucine (L) Methionine (M) Valine (V) 6 Phenylalanine (F) Tyrosine
(Y) Trytophan (W)
[0183] Nucleic Acid Hybridization
[0184] Comparative hybridization can be used to identify nucleic
acids of the invention, including conservative variations of
nucleic acids of the invention, and this comparative hybridization
method is a preferred method of distinguishing nucleic acids of the
invention. In addition, target nucleic acids which hybridize to the
nucleic acids represented by SEQ ID NO:1-3 or SEQ ID NO:4-34 (see,
Table 5) under high, ultra-high and ultra-ultra high stringency
conditions are a feature of the invention. Examples of such nucleic
acids include those with one or a few silent or conservative
nucleic acid substitutions as compared to a given nucleic acid
sequence.
[0185] A test nucleic acid is said to specifically hybridize to a
probe nucleic acid when it hybridizes at least 1/2 as well to the
probe as to the perfectly matched complementary target, i.e., with
a signal to noise ratio at lest 1/2 as high as hybridization of the
probe to the target under conditions in which the perfectly matched
probe binds to the perfectly matched complementary target with a
signal to noise ratio that is at least about 5.times.-10.times. as
high as that observed for hybridization to any of the unmatched
target nucleic acids.
[0186] Nucleic acids "hybridize" when they associate, typically in
solution. Nucleic acids hybridize due to a variety of well
characterized physico-chemical forces, such as hydrogen bonding,
solvent exclusion, base stacking and the like. An extensive guide
to the hybridization of nucleic acids is found in Tijssen (1993)
Laboratory Techniques in Biochemistry and Molecular
Biology--Hybridization with Nucleic Acid Probes part I chapter 2,
"Overview of principles of hybridization and the strategy of
nucleic acid probe assays," (Elsevier, New York), as well as in
Ausubel, infra. Hames and Higgins (1995) Gene Probes 1 IRL Press at
Oxford University Press, Oxford, England, (Hames and Higgins 1) and
Hames and Higgins (1995) Gene Probes 2 IRL Press at Oxford
University Press, Oxford, England (Hames and Higgins 2) provide
details on the synthesis, labeling, detection and quantification of
DNA and RNA, including oligonucleotides.
[0187] An example of stringent hybridization conditions for
hybridization of complementary nucleic acids which have more than
100 complementary residues on a filter in a Southern or northern
blot is 50% formalin with 1 mg of heparin at 42.degree. C., with
the hybridization being carried out overnight. An example of
stringent wash conditions is a 0.2.times.SSC wash at 65.degree. C.
for 15 minutes (see, Sambrook, infra for a description of SSC
buffer). Often the high stringency wash is preceded by a low
stringency wash to remove background probe signal. An example low
stringency wash is 2.times.SSC at 40.degree. C. for 15 minutes. In
general, a signal to noise ratio of 5.times. (or higher) than that
observed for an unrelated probe in the particular hybridization
assay indicates detection of a specific hybridization.
[0188] "Stringent hybridization wash conditions" in the context of
nucleic acid hybridization experiments such as Southern and
northern hybridizations are sequence dependent, and are different
under different environmental parameters. An extensive guide to the
hybridization of nucleic acids is found in Tijssen (1993), supra.
and in Hames and Higgins, 1 and 2. Stringent hybridization and wash
conditions can easily be determined empirically for any test
nucleic acid. For example, in determining highly stringent
hybridization and wash conditions, the hybridization and wash
conditions are gradually increased (e.g., by increasing
temperature, decreasing salt concentration, increasing detergent
concentration and/or increasing the concentration of organic
solvents such as formalin in the hybridization or wash), until a
selected set of criteria are met. For example, the hybridization
and wash conditions are gradually increased until a probe binds to
a perfectly matched complementary target with a signal to noise
ratio that is at least 5.times. as high as that observed for
hybridization of the probe to an unmatched target.
[0189] "Very stringent" conditions are selected to be equal to the
thermal melting point (T.sub.m) for a particular probe. The T.sub.m
is the temperature (under defined ionic strength and pH) at which
50% of the test sequence hybridizes to a perfectly matched probe.
For the purposes of the present invention, generally, "highly
stringent" hybridization and wash conditions are selected to be
about 5.degree. C. lower than the T.sub.m for the specific sequence
at a defined ionic strength and pH.
[0190] "Ultra high-stringency" hybridization and wash conditions
are those in which the stringency of hybridization and wash
conditions are increased until the signal to noise ratio for
binding of the probe to the perfectly matched complementary target
nucleic acid is at least 10.times. as high as that observed for
hybridization to any of the unmatched target nucleic acids. A
target nucleic acid which hybridizes to a probe under such
conditions, with a signal to noise ratio of at least 1/2 that of
the perfectly matched complementary target nucleic acid is said to
bind to the probe under ultra-high stringency conditions.
[0191] Similarly, even higher levels of stringency can be
determined by gradually increasing the hybridization and/or wash
conditions of the relevant hybridization assay. For example, those
in which the stringency of hybridization and wash conditions are
increased until the signal to noise ratio for binding of the probe
to the perfectly matched complementary target nucleic acid is at
least 10.times., 20.times., 50.times., 100.times., or 500.times. or
more as high as that observed for hybridization to any of the
unmatched target nucleic acids. A target nucleic acid which
hybridizes to a probe under such conditions, with a signal to noise
ratio of at least 1/2 that of the perfectly matched complementary
target nucleic acid is said to bind to the probe under
ultra-ultra-high stringency conditions.
[0192] Nucleic acids which do not hybridize to each other under
stringent conditions are still substantially identical if the
polypeptides which they encode are substantially identical. This
occurs, e.g., when a copy of a nucleic acid is created using the
maximum codon degeneracy permitted by the genetic code.
[0193] Unique Subsequences
[0194] In one aspect, the invention provides a nucleic acid which
comprises a unique subsequence in a nucleic acid selected from the
sequences of O-tRNAs and O-RSs disclosed herein, e.g., SEQ ID
NO:1-3 or SEQ ID NO:4-34 (see, Table 5). The unique subsequence is
unique as compared to a nucleic acid corresponding to any
previously known O-tRNA or O-RS nucleic acid sequence, e.g., as
found in Genbank. Alignment can be performed using, e.g., BLAST set
to default parameters. Any unique subsequence is useful, e.g., as a
probe to identify the nucleic acids of the invention.
[0195] Similarly, the invention includes a polypeptide which
comprises a unique subsequence in a polypeptide selected from the
sequences of O-RSs disclosed herein, e.g., SEQ ID NO:35-66 (see,
Table 5). Here, the unique subsequence is unique as compared to a
polypeptide corresponding to any of known polypeptide sequence.
[0196] The invention also provides for target nucleic acids which
hybridizes under stringent conditions to a unique coding
oligonucleotide which encodes a unique subsequence in a polypeptide
selected from the sequences of O-RSs wherein the unique subsequence
is unique as compared to a polypeptide corresponding to any of the
control polypeptides. Unique sequences are determined as noted
above.
[0197] Sequence Comparison, Identity, and Homology
[0198] The terms "identical" or percent "identity," in the context
of two or more nucleic acid or polypeptide sequences, refer to two
or more sequences or subsequences that are the same or have a
specified percentage of amino acid residues or nucleotides that are
the same, when compared and aligned for maximum correspondence, as
measured using one of the sequence comparison algorithms described
below (or other algorithms available to persons of skill) or by
visual inspection.
[0199] The phrase "substantially identical," in the context of two
nucleic acids or polypeptides (e.g., DNAs encoding an O-tRNA or
O-RS, or the amino acid sequence of an O-RS) refers to two or more
sequences or subsequences that have at least about 60%, preferably
80%, most preferably 90-95% nucleotide or amino acid residue
identity, when compared and aligned for maximum correspondence, as
measured using a sequence comparison algorithm or by visual
inspection. Such "substantially identical" sequences are typically
considered to be "homologous," without reference to actual
ancestry. Preferably, "substantial identity" exists over a region
of the sequences that is at least about 50 residues in length, more
preferably over a region of at least about 100 residues, and most
preferably the sequences are substantially identical over at least
about 150 residues, or over the full length of the two sequences to
be compared.
[0200] For sequence comparison and homology determination,
typically one sequence acts as a reference sequence to which test
sequences are compared. When using a sequence comparison algorithm,
test and reference sequences are input into a computer, subsequence
coordinates are designated, if necessary, and sequence algorithm
program parameters are designated. The sequence comparison
algorithm then calculates the percent sequence identity for the
test sequence(s) relative to the reference sequence, based on the
designated program parameters.
[0201] Optimal alignment of sequences for comparison can be
conducted, e.g., by the local homology algorithm of Smith &
Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment
algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),
by the search for similarity method of Pearson & Lipman, Proc.
Natl. Acad. Sci. USA 85:2444 (1988), by computerized
implementations of these algorithms (GAP, BESTFIT, FASTA, and
TFASTA in the Wisconsin Genetics Software Package, Genetics
Computer Group, 575 Science Dr., Madison, Wis.), or by visual
inspection (see generally, Ausubel et al., infra).
[0202] One example of an algorithm that is suitable for determining
percent sequence identity and sequence similarity is the BLAST
algorithm, which is described in Altschul et al., J. Mol. Biol.
215:403-410 (1990). Software for performing BLAST analyses is
publicly available through the National Center for Biotechnology
Information (www.ncbi.nlm.nih.gov/). This algorithm involves first
identifying high scoring sequence pairs (HSPs) by identifying short
words of length W in the query sequence, which either match or
satisfy some positive-valued threshold score T when aligned with a
word of the same length in a database sequence. T is referred to as
the neighborhood word score threshold (Altschul et al., supra).
These initial neighborhood word hits act as seeds for initiating
searches to find longer HSPs containing them. The word hits are
then extended in both directions along each sequence for as far as
the cumulative alignment score can be increased. Cumulative scores
are calculated using, for nucleotide sequences, the parameters M
(reward score for a pair of matching residues; always >0) and N
(penalty score for mismatching residues; always <0). For amino
acid sequences, a scoring matrix is used to calculate the
cumulative score. Extension of the word hits in each direction are
halted when: the cumulative alignment score falls off by the
quantity X from its maximum achieved value; the cumulative score
goes to zero or below, due to the accumulation of one or more
negative-scoring residue alignments; or the end of either sequence
is reached. The BLAST algorithm parameters W, T, and X determine
the sensitivity and speed of the alignment. The BLASTN program (for
nucleotide sequences) uses as defaults a wordlength (W) of 11, an
expectation (E) of 10, a cutoff of 100, M=5, N=4, and a comparison
of both strands. For amino acid sequences, the BLASTP program uses
as defaults a wordlength (W) of 3, an expectation (E) of 10, and
the BLOSUM62 scoring matrix (see, Henikoff & Henikoff (1989)
Proc. Natl. Acad. Sci. USA 89:10915).
[0203] In addition to calculating percent sequence identity, the
BLAST algorithm also performs a statistical analysis of the
similarity between two sequences (see, e.g., Karlin & Altschul,
Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of
similarity provided by the BLAST algorithm is the smallest sum
probability (P(N)), which provides an indication of the probability
by which a match between two nucleotide or amino acid sequences
would occur by chance. For example, a nucleic acid is considered
similar to a reference sequence if the smallest sum probability in
a comparison of the test nucleic acid to the reference nucleic acid
is less than about 0.1, more preferably less than about 0.01, and
most preferably less than about 0.001.
[0204] Defining Polypeptides by Immunoreactivity
[0205] Because the polypeptides of the invention provide a variety
of new polypeptide sequences (e.g., comprising unnatural amino
acids in the case of proteins synthesized in the translation
systems herein, or, e.g., in the case of the novel synthetases
herein, novel sequences of standard amino acids), the polypeptides
also provide new structural features which can be recognized, e.g.,
in immunological assays. The generation of antisera which
specifically bind the polypeptides of the invention, as well as the
polypeptides which are bound by such antisera, are a feature of the
invention.
[0206] For example, the invention includes synthetase proteins that
specifically bind to or that are specifically immunoreactive with
an antibody or antisera generated against an immunogen comprising
an amino acid sequence selected from one or more SEQ ID NO:35-66
(see, Table 5). To eliminate cross-reactivity with other
homologues, the antibody or antisera is subtracted with available
synthetases, such as the wild-type Methanococcus jannaschii (M.
jannaschii) tyrosyl synthetase (TyrRS), e.g., the "control"
polypeptides. Where the the wild-type Methanococcus jannaschii (M.
jannaschii) tyrosyl synthetase (TyrRS) corresponds to a nucleic
acid, a polypeptide encoded by the nucleic acid is generated and
used for antibody/antisera subtraction purposes.
[0207] In one typical format, the immunoassay uses a polyclonal
antiserum which was raised against one or more polypeptide
comprising one or more of the sequences corresponding to one or
more of SEQ ID NO:35-66 (see, Table 5) or a substantial subsequence
thereof (i.e., at least about 30% of the full length sequence
provided). The set of potential polypeptide immunogens derived from
SEQ ID NO:35-66 (see, Table 5) are collectively referred to below
as "the immunogenic polypeptides." The resulting antisera is
optionally selected to have low cross-reactivity against the
control synthetase homologues and any such cross-reactivity is
removed, e.g., by immunoabsorbtion, with one or more of the control
synthetase homologues, prior to use of the polyclonal antiserum in
the immunoassay.
[0208] In order to produce antisera for use in an immunoassay, one
or more of the immunogenic polypeptides is produced and purified as
described herein. For example, recombinant protein can be produced
in a recombinant cell. An inbred strain of mice (used in this assay
because results are more reproducible due to the virtual genetic
identity of the mice) is immunized with the immunogenic protein(s)
in combination with a standard adjuvant, such as Freund's adjuvant,
and a standard mouse immunization protocol (see, e.g., Harlow and
Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor
Publications, New York, for a standard description of antibody
generation, immunoassay formats and conditions that can be used to
determine specific immunoreactivity. Additional references and
discussion of antibodies is also found herein and can be applied
here to defining polypeptides by immunoreactivity). Alternatively,
one or more synthetic or recombinant polypeptide derived from the
sequences disclosed herein is conjugated to a carrier protein and
used as an immunogen.
[0209] Polyclonal sera are collected and titered against the
immunogenic polypeptide in an immunoassay, for example, a solid
phase immunoassay with one or more of the immunogenic proteins
immobilized on a solid support. Polyclonal antisera with a titer of
10.sup.6 or greater are selected, pooled and subtracted with the
control synthetase polypeptides to produce subtracted pooled
titered polyclonal antisera.
[0210] The subtracted pooled titered polyclonal antisera are tested
for cross reactivity against the control homologues in a
comparative immunoassay. In this comparative assay, discriminatory
binding conditions are determined for the subtracted titered
polyclonal antisera which result in at least about a 5-10 fold
higher signal to noise ratio for binding of the titered polyclonal
antisera to the immunogenic synthetase as compared to binding to
the control synthetase homologues. That is, the stringency of the
binding reaction is adjusted by the addition of non-specific
competitors such as albumin or non-fat dry milk, and/or by
adjusting salt conditions, temperature, and/or the like. These
binding conditions are used in subsequent assays for determining
whether a test polypeptide (a polypeptide being compared to the
immunogenic polypeptides and/or the control polypeptides) is
specifically bound by the pooled subtracted polyclonal antisera. In
particular, test polypeptides which show at least a 2-5.times.
higher signal to noise ratio than the control synthetase homologues
under discriminatory binding conditions, and at least about a 1/2
signal to noise ratio as compared to the immunogenic
polypeptide(s), shares substantial structural similarity with the
immunogenic polypeptide as compared to known synthetases, and is,
therefore a polypeptide of the invention.
[0211] In another example, immunoassays in the competitive binding
format are used for detection of a test polypeptide. For example,
as noted, cross-reacting antibodies are removed from the pooled
antisera mixture by immunoabsorbtion with the control polypeptides.
The immunogenic polypeptide(s) are then immobilized to a solid
support which is exposed to the subtracted pooled antisera. Test
proteins are added to the assay to compete for binding to the
pooled subtracted antisera. The ability of the test protein(s) to
compete for binding to the pooled subtracted antisera as compared
to the immobilized protein(s) is compared to the ability of the
immunogenic polypeptide(s) added to the assay to compete for
binding (the immunogenic polypeptides compete effectively with the
immobilized immunogenic polypeptides for binding to the pooled
antisera). The percent cross-reactivity for the test proteins is
calculated, using standard calculations.
[0212] In a parallel assay, the ability of the control proteins to
compete for binding to the pooled subtracted antisera is optionally
determined as compared to the ability of the immunogenic
polypeptide(s) to compete for binding to the antisera. Again, the
percent cross-reactivity for the control polypeptides is
calculated, using standard calculations. Where the percent
cross-reactivity is at least 5-10.times. as high for the test
polypeptides as compared to the control polypeptides and or where
the binding of the test polypeptides is approximately in the range
of the binding of the immunogenic polypeptides, the test
polypeptides are said to specifically bind the pooled subtracted
antisera.
[0213] In general, the immunoabsorbed and pooled antisera can be
used in a competitive binding immunoassay as described herein to
compare any test polypeptide to the immunogenic and/or control
polypeptide(s). In order to make this comparison, the immunogenic,
test and control polypeptides are each assayed at a wide range of
concentrations and the amount of each polypeptide required to
inhibit 50% of the binding of the subtracted antisera to, e.g., an
immobilized control, test or immunogenic protein is determined
using standard techniques. If the amount of the test polypeptide
required for binding in the competitive assay is less than twice
the amount of the immunogenic polypeptide that is required, then
the test polypeptide is said to specifically bind to an antibody
generated to the immunogenic protein, provided the amount is at
least about 5-10.times. as high as for the control polypeptide.
[0214] As an additional determination of specificity, the pooled
antisera is optionally fully immunosorbed with the immunogenic
polypeptide(s) (rather than the control polypeptides) until little
or no binding of the resulting immunogenic polypeptide subtracted
pooled antisera to the immunogenic polypeptide(s) used in the
immunosorbtion is detectable. This fully immunosorbed antisera is
then tested for reactivity with the test polypeptide. If little or
no reactivity is observed (i.e., no more than 2.times. the signal
to noise ratio observed for binding of the fully immunosorbed
antisera to the immunogenic polypeptide), then the test polypeptide
is specifically bound by the antisera elicited by the immunogenic
protein.
[0215] General Techniques
[0216] General texts which describe molecular biological
techniques, which are applicable to the present invention, such as
cloning, mutation, cell culture and the like, include Berger and
Kimmel, Guide to Molecular Cloning Techniques, Methods in
Enzymology volume 152 Academic Press, Inc., San Diego, Calif.
(Berger); Sambrook et al., Molecular Cloning--A Laboratory Manual
(3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring
Harbor, N.Y., 2000 ("Sambrook") and Current Protocols in Molecular
Biology, F. M. Ausubel et al., eds., Current Protocols, a joint
venture between Greene Publishing Associates, Inc. and John Wiley
& Sons, Inc., (supplemented through 2002) ("Ausubel")). These
texts describe mutagenesis, the use of vectors, promoters and many
other relevant topics related to, e.g., the generation of
orthogonal tRNA, orthogonal synthetases, and pairs thereof.
[0217] Various types of mutagenesis are used in the present
invention, e.g., to produce novel sythetases or tRNAs. They include
but are not limited to site-directed, random point mutagenesis,
homologous recombination (DNA shuffling), mutagenesis using uracil
containing templates, oligonucleotide-directed mutagenesis,
phosphorothioate-modifie- d DNA mutagenesis, mutagenesis using
gapped duplex DNA or the like. Additional suitable methods include
point mismatch repair, mutagenesis using repair-deficient host
strains, restriction-selection and restriction-purification,
deletion mutagenesis, mutagenesis by total gene synthesis,
double-strand break repair, and the like. Mutagenesis, e.g.,
involving chimeric constructs, are also included in the present
invention. In one embodiment, mutagenesis can be guided by known
information of the naturally occurring molecule or altered or
mutated naturally occurring molecule, e.g., sequence, sequence
comparisons, physical properties, crystal structure or the
like.
[0218] The above texts and examples found herein describe these
procedures as well as the following publications and references
cited within: Sieber, et al., Nature Biotechnology, 19:456460
(2001); Ling et al., Approaches to DNA mutagenesis: an overview,
Anal Biochem. 254(2): 157-178 (1997); Dale et al.,
Oligonucleotide-directed random mutagenesis using the
phosphorothioate method, Methods Mol. Biol. 57:369-374 (1996); I.
A. Lorimer, I. Pastan, Nucleic Acids Res. 23, 3067-8 (1995); W. P.
C. Stemmer, Nature 370, 389-91 (1994); Arnold, Protein engineering
for unusual environments, Current Opinion in Biotechnology
4:450-455 (1993); Bass et al., Mutant Trp repressors with new
DNA-binding specificities, Science 242:240-245 (1988); Fritz et
al., Oligonucleotide-directed construction of mutations: a gapped
duplex DNA procedure without enzymatic reactions in vitro, Nucl.
Acids Res. 16: 6987-6999 (1988); Kramer et al., Improved enzymatic
in vitro reactions in the gapped duplex DNA approach to
oligonucleotide-directed construction of mutations, Nucl. Acids
Res. 16: 7207 (1988); Sakamar and Khorana, Total synthesis and
expression of a gene for the .alpha.-subunit of bovine rod outer
segment guanine nucleotide-binding protein (transducin), Nucl.
Acids Res. 14: 6361-6372 (1988); Sayers et al., Y-T Exonucleases in
phosphorothioate-based oligonucleotide-directed mutagenesis, Nucl.
Acids Res. 16:791-802 (1988); Sayers et al., Strand specific
cleavage of phosphorothioate-containing DNA by reaction with
restriction endonucleases in the presence of ethidium bromide,
(1988) Nucl. Acids Res. 16: 803-814; Carter, Improved
oligonucleotide-directed mutagenesis using M13 vectors, Methods in
Enzymol. 154: 382403 (1987); Kramer & Fritz
Oligonucleotide-directed construction of mutations via gapped
duplex DNA, Methods in Enzymol. 154:350-367 (1987); Kunkel, The
efficiency of oligonucleotide directed mutagenesis, in Nucleic
Acids & Molecular Biology (Eckstein, F. and Lilley, D. M. J.
eds., Springer Verlag, Berlin)) (1987); Kunkel et al., Rapid and
efficient site-specific mutagenesis without phenotypic selection,
Methods in Enzymol. 154, 367-382 (1987); Zoller & Smith,
Oligonucleotide-directed mutagenesis: a simple method using two
oligonucleotide primers and a single-stranded DNA template, Methods
in Enzymol. 154:329-350 (1987); Carter, Site-directed mutagenesis,
Biochem. J. 237:1-7 (1986); Eghtedarzadeh & Henikoff, Use of
oligonucleotides to generate large deletions, Nucl. Acids Res. 14:
5115 (1986); Mandecki, Oligonucleotide-directed double-strand break
repair in plasmids of Escherichia coli: a method for site-specific
mutagenesis, Proc. Natl. Acad. Sci. USA, 83:7177-7181 (1986);
Nakamaye & Eckstein, Inhibition of restriction endonuclease Nci
I cleavage by phosphorothioate groups and its application to
oligonucleotide-directed mutagenesis, Nucl. Acids Res. 14:
9679-9698 (1986); Wells et al., Importance of hydrogen-bond
formation in stabilizing the transition state of subtilisin, Phil.
Trans. R. Soc. Lond. A 317: 415423 (1986); Botstein & Shortle,
Strategies and applications of in vitro mutagenesis, Science
229:1193-1201 (1985); Carter et al., Improved oligonucleotide
site-directed mutagenesis using M13 vectors, Nucl. Acids Res. 13:
4431-413 (1985); Grundstrom et al., Oligonucleotide-directed
mutagenesis by microscale `shot-gun` gene synthesis, Nucl. Acids
Res. 13: 3305-3316 (1985); Kunkel, Rapid and efficient
site-specific mutagenesis without phenotypic selection, Proc. Natl.
Acad. Sci. USA 82:488492 (1985); Smith, In vitro mutagenesis, Ann.
Rev. Genet. 19:423462 (1985); Taylor et al., The use of
phosphorothioate-modified DNA in restriction enzyme reactions to
prepare nicked DNA, Nucl. Acids Res. 13: 8749-8764 (1985); Taylor
et al., The rapid generation of oligonucleotide-directed mutations
at high frequency using phosphorothioate-modified DNA, Nucl. Acids
Res. 13: 8765-8787 (1985); Wells et al., Cassette mutagenesis: an
efficient method for generation of multiple mutations at defined
sites, Gene 34:315-323 (1985); Kramer et al., The gapped duplex DNA
approach to oligonucleotide-directed mutation construction, Nucl.
Acids Res. 12: 9441-9456 (1984); Kramer et al., Point Mismatch
Repair, Cell 38:879-887 (1984); Nambiar et al., Total synthesis and
cloning of a gene coding for the ribonuclease S protein, Science
223: 1299-1301 (1984); Zoller & Smith, Oligonucleotide-directed
mutagenesis of DNA fragments cloned into M13 vectors, Methods in
Enzymol. 100:468-500 (1983); and Zoller & Smith,
Oligonucleotide-directed mutagenesis using M13-derived vectors: an
efficient and general procedure for the production of point
mutations in any DNA fragment, Nucleic Acids Res. 10:6487-6500
(1982). Additional details on many of the above methods can be
found in Methods in Enzymology Volume 154, which also describes
useful controls for trouble-shooting problems with various
mutagenesis methods.
[0219] Oligonucleotides, e.g., for use in mutagenesis of the
present invention, e.g., mutating libraries of synthetases, or
altering tRNAs, are typically synthesized chemically according to
the solid phase phosphoramidite triester method described by
Beaucage and Caruthers, Tetrahedron Letts. 22(20):1859-1862, (1981)
e.g., using an automated synthesizer, as described in
Needham-VanDevanter et al., Nucleic Acids Res., 12:6159-6168
(1984).
[0220] In addition, essentially any nucleic acid can be custom or
standard ordered from any of a variety of commercial sources, such
as The Midland Certified Reagent Company (mcrc@oligos.com), The
Great American Gene Company (www.genco.com), ExpressGen Inc.
(www.expressgen.com), Operon Technologies Inc. (Alameda, Calif.)
and many others.
[0221] The present invention also relates to host cells and
organisms for the in vivo incorporation of an unnatural amino acid
via orthogonal tRNA/RS pairs. Host cells are genetically engineered
(e.g., transformed, transduced or transfected) with the vectors of
this invention, which can be, for example, a cloning vector or an
expression vector. The vector can be, for example, in the form of a
plasmid, a bacterium, a virus, a naked polynucleotide, or a
conjugated polynucleotide. The vectors are introduced into cells
and/or microorganisms by standard methods including electroporation
(From et al., Proc. Natl. Acad. Sci. USA 82, 5824 (1985), infection
by viral vectors, high velocity ballistic penetration by small
particles with the nucleic acid either within the matrix of small
beads or particles, or on the surface (Klein et al., Nature 327,
70-73 (1987)). Berger, Sambrook, and Ausubel provide a variety of
appropriate transformation methods.
[0222] The engineered host cells can be cultured in conventional
nutrient media modified as appropriate for such activities as, for
example, screening steps, activating promoters or selecting
transformants. These cells can optionally be cultured into
transgenic organisms.
[0223] Other useful references, e.g. for cell isolation and culture
(e.g., for subsequent nucleic acid isolation) include Freshney
(1994) Culture of Animal Cells, a Manual of Basic Technique, third
edition, Wiley-Liss, New York and the references cited therein;
Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems
John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips
(eds.) (1995) Plant Cell, Tissue and Organ Culture; Fundamental
Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg New
York) and Atlas and Parks (eds.) The Handbook of Microbiological
Media (1993) CRC Press, Boca Raton, Fla.
[0224] Several well-known methods of introducing target nucleic
acids into bacterial cells are available, any of which can be used
in the present invention. These include: fusion of the recipient
cells with bacterial protoplasts containing the DNA,
electroporation, projectile bombardment, and infection with viral
vectors, etc. Bacterial cells can be used to amplify the number of
plasmids containing DNA constructs of this invention. The bacteria
are grown to log phase and the plasmids within the bacteria can be
isolated by a variety of methods known in the art (see, for
instance, Sambrook). In addition, a plethora of kits are
commercially available for the purification of plasmids from
bacteria, (see, e.g., EasyPrep.TM., FlexiPrep.TM., both from
Pharmacia Biotech; StrataClean.TM., from Stratagene; and,
QIAprep.TM. from Qiagen). The isolated and purified plasmids are
then further manipulated to produce other plasmids, used to
transfect cells or incorporated into related vectors to infect
organisms. Typical vectors contain transcription and translation
terminators, transcription and translation initiation sequences,
and promoters useful for regulation of the expression of the
particular target nucleic acid. The vectors optionally comprise
generic expression cassettes containing at least one independent
terminator sequence, sequences permitting replication of the
cassette in eukaryotes, or prokaryotes, or both, (e.g., shuttle
vectors) and selection markers for both prokaryotic and eukaryotic
systems. Vectors are suitable for replication and integration in
prokaryotes, eukaryotes, or preferably both. See, Giliman &
Smith, Gene 8:81 (1979); Roberts, et al., Nature, 328:731 (1987);
Schneider, B., et al., Protein Expr. Purif. 6435:10 (1995);
Ausubel, Sambrook, Berger (all supra). A catalogue of Bacteria and
Bacteriophages useful for cloning is provided, e.g., by the ATCC,
e.g., The ATCC Catalogue of Bacteria and Bacteriophage (1992) Ghema
et al. (eds.) published by the ATCC. Additional basic procedures
for sequencing, cloning and other aspects of molecular biology and
underlying theoretical considerations are also found in Watson et
al. (1992) Recombinant DNA Second Edition Scientific American
Books, NY.
EXAMPLES
[0225] The following examples are offered to illustrate, but not to
limit the claimed invention.
Example 1
Improvement of Orthogonality of a tRNA from Methanococcus
jannaschii
[0226] Because of the complex nature of tRNA-synthetase
interactions that are required to achieve a high degree of fidelity
in protein translation, the rational design of orthogonal
tRNA-synthetase pairs is difficult. This example describes methods
that exploit the poor cross recognition of some interspecies
tRNA-synthetase pairs, coupled with subsequent in vivo evolution of
tRNAs with enhanced orthogonality. See, also, L. Wang and P. G.
Schultz, Chem. Biol., 8:883 (2001). Specifically, a library of
amber suppressor tRNAs derived from Methanococcus jannaschii
tRNATyr was generated. tRNATyrCUAs that are substrates for
endogenous Escherichia coli aminoacyl-tRNA synthetases were deleted
from the pool by negative selection based on suppression of amber
nonsense mutations in the barnase gene. The remaining tRNATyrCUAs
were then selected for their ability to suppress amber nonsense
codons in the .beta.-lactamase gene in the presence of the cognate
Methanococcus jannaschii tyrosyl-tRNA synthetase (TyrRS). Four
mutant suppressor tRNAs were selected that are poorer substrates
for Escherichia coli synthetases than Methanococcus jannaschii
tRNATyrCUA, but still can be charged efficiently by Methanococcus
jannaschii TyrRS. The mutant suppressor tRNATyrCUA together with
the Methanococcus jannaschii TyrRS provide a useful orthogonal
tRNA-synthetase pair for the in vivo incorporation of unnatural
amino acids into proteins.
[0227] The tRNATyr of Methanococcus jannaschii, an archaebacterium,
has different identity elements from those of Escherichia coli
tRNATyr. In particular, the Escherichia coli tRNATyr has a G1C72
pair in the acceptor stem while the Methanococcus jannaschii
tRNATyr has a C1G72 pair. An amber suppressor tRNA derived from
Methanococcus jannaschii tRNATyr was shown not to be efficiently
aminoacylated by the Escherichia coli synthetases, but functions
efficiently in protein translation in Escherichia coli. See, e.g.,
L. Wang, T. J. Magliery, D. R. Liu, P. G. Schultz, A new functional
suppressor tRNA/aminoacyl-tRNA synthetase pair for the in vivo
incorporation of unnatural amino acids into proteins, J. Am. Chem.
Soc. 122:5010-5011 (2000). In addition, the Methanococcus
jannaschii TyrRS, which has only a minimalist
anticodon-loop-binding domain, does not aminoacylate Escherichia
coli tRNAs, but still efficiently aminoacylates its own suppressor
tRNATyrCUA. See, e.g., B. A. Steer, P. Schimmel, Major
anticodon-binding region missing from an archaebacterial tRNA
synthetase, J. Biol. Chem. 274 (1999) 35601-35606; and, Wang et
al., (2000), supra.
[0228] To test the orthogonality of this suppressor tRNA in
Escherichia coli, an amber codon was introduced at a permissive
site (Ala184) in the .beta.-lactamase gene. See, e.g., D. R. Liu,
P. G. Schultz, Progress toward the evolution of an organism with an
expanded genetic code, Proc. Natl. Acad. Sci. USA 96:4780-4785
(1999). Those tRNAs that can be charged by Escherichia coli
synthetases will suppress the amber codon and allow cells to live
in the presence of ampicillin. The Methanococcus jannaschii
tRNATyrCUA suppresses the amber codon in the .beta.-lactamase gene
with an IC.sub.50 value of 56 .mu.g/ml ampicillin. See Wang et al.,
(2000), supra. In contrast, the orthogonal tRNAGlnCUA derived from
Saccharomyces cerevisiae tRNAGln2 has an IC.sub.50 of 21 .mu.g/ml
ampicillin when tested in the same assay. See Liu & Schultz,
(1999), supra. The IC.sub.50 for Escherichia coli in the absence of
any suppressor tRNA is 10 .mu.g/ml ampicillin. This result shows
that the Methanococcus jannaschii tRNATyrCUA is a better substrate
for Escherichia coli synthetases than the tRNAGlnCUA. Consequently,
if the Methanococcus jannaschii tRNATyrCUA is used in vivo to
deliver unnatural amino acids into proteins in Escherichia coli, it
can also be mischarged with natural amino acids by Escherichia coli
synthetases, leading to heterogeneous amino acid incorporation.
[0229] The improvement of the orthogonality of the Methanococcus
jannaschii tRNATyrCUA was accomplished by the introduction of
`negative recognition determinants` to prevent recognition by
endogenous Escherichia coli synthetases. These mutations should not
strongly interfere with the tRNA's interaction with its cognate
Methanococcus jannaschii TyrRS or the ribosome. Since Methanococcus
jannaschii TyrRS lacks most of the anticodon-binding domain, see,
e.g., B. A. Steer, P. Schimmel, Major anticodon-binding region
missing from an archaebacterial tRNA synthetase, J. Biol. Chem.
274:35601-35606 (1999), mutations introduced at the anticodon loop
of the tRNA are expected to have a minimal effect on TyrRS
recognition. An anticodon-loop library with four randomized
nucleotides was constructed. See FIG. 9. Given the various
combinations and locations of identity elements for various
Escherichia coli tRNAs, mutations at additional positions can
increase the likelihood of finding a mutant tRNA with the desired
properties. Thus, a second library containing mutations at
nonconserved positions in all of the tRNA loops (all-loop library)
was also constructed. See FIG. 9. Conserved nucleotides were not
randomized so as to maintain the tertiary interactions that
stabilize the `L`-shaped structure of the tRNA. See, e.g., G.
Dirheimer, G. Keith, P. Dumas, E. Westhof, Primary, secondary, and
tertiary structures of tRNAs, in: D. Soll, U. L. RajBhandary
(eds.), tRNA Structure, Biosynthesis, and Function, ASM Press,
Washington, D.C., 1995, pp. 93-126; and, R. Giege, M. Sissler, C.
Florentz, Universal rules and idiosyncratic features in tRNA
identity, Nucleic Acids Res. 26:5017-5035 (1998). Stem nucleotides
were also not mutated since substitution of one such nucleotide
requires a compensatory mutation. The 11 nucleotides (C16, C17,
U17a, U20, C32, G37, A38, U45, U47, A59, and U60) were randomized.
See, FIG. 9. The theoretical size of this library is about
4.19.times.10.sup.6, and a library with a size of about
1.93.times.10.sup.8 colony-forming units was constructed to ensure
complete coverage of the mutant library.
[0230] The methods used an Escherichia coli strain, e.g., DH10B,
which was obtained from Gibco/BRL. Suppressor tRNA expression
plasmids were derived from a plasmid, e.g., pAC123. See, e.g., D.
R. Liu, T. J. Magliery, M. Pastrnak, P. G. Schultz, Engineering a
tRNA and aminoacyl-tRNA synthetase for the site-specific
incorporation of unnatural amino acids into proteins in vivo, Proc.
Natl. Acad. Sci. USA 94:10091-10097 (1997). Plasmids for negative
selections were derived from plasmids, e.g., pBATS, pYsupA38B2 and
pYsupA38B3 as described below. See, e.g., K. Gabriel, W. H.
McClain, A set of plasmids constitutively producing different RNA
levels in Escherichia coli, J. Mol. Biol. 290 (1999) 385-389; and,
Liu & Shultz, (1999), supra.
[0231] To select for a member of the Methanococcus jannaschii tRNA
library with enhanced orthogonality, a combination of negative and
positive selections in the absence and presence of the cognate
synthetase was used. See FIG. 8. In the negative selection,
selector codon(s), e.g., amber nonsense, are introduced in a
negative marker gene, e.g., a toxic gene, at e.g., a nonessential
position. When a member of the mutated, e.g., suppressor, tRNA
library is aminoacylated by endogenous (e.g., Escherichia coli)
synthetases (i.e. it is not orthogonal to the Escherichia coli
synthetases), the selector codon is suppressed and the toxic gene
product produced leads to cell death. Only cells harboring
orthogonal tRNAs or nonfunctional tRNAs can survive. All survivors
are then subjected to a positive selection in which a selector
codon, e.g., an amber codon, is placed in a positive selection
marker, e.g., drug resistance gene at, e.g., a nonessential
position. tRNAs are then selected for their ability to be
aminoacylated by the coexpressed cognate synthetase and to insert
an amino acid in response to this amber codon. Cells harboring
nonfunctional tRNAs, or tRNAs that cannot be recognized by the
synthetase of interest will be sensitive to antibiotic. Therefore,
only tRNAs that (1) are not substrates for endogenous Escherichia
coli synthetases; (2) can be aminoacylated by the synthetase of
interest; (3) are functional in translation will survive both
selections.
[0232] A negative selection was chosen that takes advantage of the
toxicity of barnase when produced in Escherichia coli in the
absence of its natural inhibitor barstar. See, e.g., R. W. Hartley,
Barnase and barstar. Expression of its cloned inhibitor permits
expression of a cloned ribonuclease, J. Mol. Biol. 202:913-915
(1988). Amber codons were introduced at nonessential positions in
the barnase gene based on analysis of the three-dimensional
structure of barnase. See, e.g., Liu & Schultz, (1999), supra.
Because of barnase's extreme autotoxicity, a low copy number pSC101
origin was placed in the plasmid expressing barnase. In addition,
different numbers of amber codons were tested to modulate the
stringency of the selection. Plasmid pSCB2 was used to express a
barnase mutant with two amber stop codons at Gln2 and Asp44;
plasmid pSCB3 contained an additional amber stop codon at
Gly65.
[0233] For negative selection, a PCR fragment containing the
.beta.-lactamase gene and the pSC101 origin was generated from
pBATS using the following oligonucleotides: LW115,
5'-ATGCATGCTGCATTAATGAATCGGC- CAACG-3'; LW116,
5'-TCCCCGCGGAGGTGGCACTCGGGG-3'. DNA encoding barnase containing two
(residues Gln2 and Asp44) or three (residues Gln2, Asp44 and Gly65)
amber codons were obtained from pYsupA38B2 and pYsupA38B3,
respectively, by digestion with SacII and SphI. Ligation of the
above fragments afforded plasmids pSCB2 and pSCB3. The expression
of barnase was under arabinose induction. Genes encoding different
suppressor tRNAs for in vivo expression were constructed from two
overlapping synthetic oligonucleotides (Operon, Alameda, Calif.,
USA) by Klenow extension and inserted between the EcoRI and PstI
sites of pAC123 to generate pAC-YYG1 and pAC-JY, respectively,
placing transcription under control of the lpp promoter and the
rrnC terminator. pAC-Cm is the control plasmid without any tRNA. To
optimize the negative selection conditions, competent DH10B cells
harboring pSCB2 or pSCB3 were transformed by electroporation with
pAC-Cm, pAC-YYG1, and pAC-JY, separately. Single colonies were
picked and grown in 2.times.YT with chloramphenicol (Cm, 34
.mu.g/ml) and ampicillin (Amp, 100 .mu.g/ml). Cell cultures grown
overnight were washed twice with minimal media containing 1%
glycerol and 0.3 mM leucine (GMML), and resuspended in GMML with Cm
and Amp to an OD600 of 0.1. After recovering at 30.degree. C. for
10 min, into one culture (set 1) was added 20 mM of arabinose to
induce the expression of barnase; no arabinose was added to the
second culture (set 2). At different time points, a small amount of
cell culture was diluted and plated on 2.times.YT agar with Cm and
Amp to measure cell density. For negative selections of the
suppressor tRNA libraries, the pAC plasmids containing the library
were transformed into DH10B cells harboring pSCB2. Cells were
quenched by addition of SOC medium and recovered at 30.degree. C.
for 1 hour, then were washed with phosphate buffer and GMML, and
cultured in 11 GMML. After recovering at 30.degree. C. for 30 min,
Cm, Amp, and 20 mM arabinose were added. After 36 hours, cells were
pelleted and pAC plasmids were isolated and purified by agarose gel
electrophoresis.
[0234] To optimize the selection conditions, two suppressor tRNAs
were used that are known to be poorly recognized by the Escherichia
coli synthetases. A mutant suppressor tRNATyr derived from
Saccharomyces cerevisiae (sc-tRNATyrCUA, expressed in pAC-YYG1)
suppresses the amber codon (Ala184TAG) in the .beta.-lactamase
gene, affording an IC.sub.50 value of 12 .mu.g/ml ampicillin for
Escherichia coli cells; and the suppressor tRNATyr derived from
Methanococcus jannaschii (mj-tRNATyrCUA, expressed in pAC-JY)
affords an IC.sub.50 of 56 .mu.g/ml ampicillin for host cells. See,
e.g., Wang et al, (2000), supra. For comparison, the suppressor
tRNAGlnCUA derived from Saccharomyces cerevisiae tRNAGln2 has an
IC.sub.50 of 21 .mu.g/1 ml ampicillin when tested in the same
assay, and has been demonstrated to be orthogonal to Escherichia
coli synthetases in vitro and in vivo. See, e.g., Liu &
Schultz, (1999), supra. Therefore, a negative selection that
eliminates cells expressing mj-tRNATyrCUA, but allows the growth of
cells expressing sc-tRNATyrCUA deletes non-orthogonal suppressor
tRNAs. Cells were grown in liquid minimal media containing 1%
glycerol and 0.3 mM leucine (GMML) with appropriate antibiotics to
maintain plasmid pSCB2 and the pAC plasmid. Arabinose was added to
one set of cells (set 1) to induce the expression of the barnase,
while in set 2 no arabinose was added. The fraction of cells
surviving the selection was determined by the ratio of cell
densities in set 1 relative to set 2. See FIG. 11: cells harboring
the control plasmid pAC-Cm (without suppressor tRNA) and plasmid
pAC-YYG1 survived, while cells harboring plasmid pAC-JY largely
died. When plasmid pSCB3 was used, cells harboring plasmid pAC-JY
started to grow in 24 hours. Therefore, the negative selection was
carried out using pSCB2, which encodes the barnase gene containing
two amber codons under the above conditions for the library
selection.
[0235] For positive selection, a plasmid, e.g., pBLAM-JYRS was
constructed by inserting the Methanococcus jannaschii TyrRS gene
from pBSA50 between NdeI and PstI sites of pBLAM-YQRS using
oligonucleotides LW104, 5'-GGAATTCCATTAGGACGAATTTGAAATG-3'; and
LW105, 5'-AAACTGCAGTTATAATCTCTITC- TAATTGGCTC-3'. See, e.g., Steer,
et al., (1999), supra; and, Liu & Schultz, (1999), supra. To
optimize the positive selection conditions, competent DH10B cells
harboring pBLAM-JYRS were transformed with pAC-Cm, pAC-YYG1, and
pAC-JY, separately. Single colonies were picked and grown in
2.times.YT with Cm and tetracycline (Tet, 40 .mu.g/ml). In liquid
selections, overnight cell cultures were diluted into 2.times.YT
with Cm and Tet at a starting OD600 of 0.1. Various concentrations
of Amp were added, and cell growth was monitored by OD600. In plate
selections, approximately 103 to 105 cells were plated on two sets
of 2.times.YT agar plates containing Cm and Tet, one set of which
contained 500 .mu.g/ml Amp. For selections involving the mutant
tRNA library, pAC plasmids isolated from the cells from the
negative selection were transformed into competent DH10B cells
harboring pBLAM-JYRS. Cells were recovered at 37.degree. C. for 45
minutes, and approximately 105 cells were plated onto each
2.times.YT agar plate containing Cm, Tet and 500 .mu.g/ml of Amp.
After 24 hours, colonies were picked and re-grown in 6 ml
2.times.YT containing Cm, Tet and 200 .mu.g/ml of Amp. DNA was
isolated and pAC plasmid was purified by agarose gel
electrophoresis.
[0236] The positive selection is based on suppression of an amber
stop codon introduced at position Ala184 in the TEM-1
.beta.-lactamase gene. Plasmid pBLAM-JYRS encodes the gene for the
Methanococcus jannaschii tyrosyl-tRNA synthetase and a lactamase
with an amber mutation at Ala184. pAC plasmids isolated from cells
surviving the negative selection were cotransformed with pBLAM-JYRS
into Escherichia coli DH10B cells. Cells harboring nonfunctional
tRNAs or tRNAs that are poor substrates for the Methanococcus
jannaschii synthetase die; those with tRNAs that can be charged by
the synthetase survive. To test the feasibility of the positive
selection, two model suppressor tRNAs were tested in the presence
of Methanococcus jannaschii TyrRS. The sc-tRNATyrCUA has a G1:C72
base pair and is not charged efficiently by Methanococcus
jannaschii TyrRS. When they were coexpressed in cells with the
Ala184amber .beta.-lactamase mutant, cells survived to an IC.sub.50
of 18 .mu.g/ml ampicillin. In contrast, cells containing the
Methanococcus jannaschii tRNATyrCUA and the cognate TyrRS survive
to an IC.sub.50 of 1220 .mu.g/ml ampicillin. See, e.g., Wang, et
al., (2000), supra. The model positive selection was first tried in
liquid 2.times.YT medium. The growth of cells harboring pBLAM-JYRS
and different pAC plasmids in liquid 2.times.YT medium with various
concentrations of ampicillin are shown in FIG. 12, Panel A. Cells
transformed with the mj-tRNATyrCUA grew at a faster rate and at
higher concentrations of ampicillin. If cells were grown longer
than 24 hours, cells transformed with either pAC-Cm or pAC-YYG1
also grew to saturation. Therefore, the positive selection was
carried out on plates with initial cell densities between 103 and
105 per plate. See FIG. 12, Panel B. The survival ratio (number of
colonies on plates with ampicillin relative to plates without
ampicillin) did not change significantly with different initial
cell densities, and was stable over the growth time. The positive
selection on ampicillin plates resulted in preferential growth of
cells with mj-tRNATyrCUA expressed. Therefore, for the library
selection the positive selection was carried out on plates instead
of in liquid medium.
[0237] The library of mutant tRNAs was generated by using the
sequences of the two overlapping oligonucleotides used to construct
the anticodon-loop library are (the tRNA sequence underlined):
LW125, 5'-GGAATIC-3'; LW126, 5'-AAAACTGCAG-3 (where N is equimolar
of A, C, T or G). The sequences of oligonucleotides for the
all-loop library are: LW145, 5'-GGAATTC-3' and LW146,
5'-AAAACTGCAG-3'. These genes were inserted into pAC123 similarly
as described above to afford the tRNA libraries.
[0238] The negative and positive selections were carried out in
tandem as described above on both the anticodon-loop and all-loop
libraries. The selected suppressor tRNAs were isolated and
retransformed into Escherichia coli DH10B harboring pBLAM to test
the tRNA's orthogonality to Escherichia coli synthetases. The tRNAs
were then retransformed into Escherichia coli harboring pBLAM-JYRS
to test how efficiently the tRNA was charged by Methanococcus
jannaschii TyrRS. Sequencing of the clones resulting from one round
of negative and positive selection of anticodon-loop library
revealed that three independent tRNAs were isolated. See FIG. 13.
When cotransformed with pBLAM, all had lower IC.sub.50 values than
the parent Methanococcus jannaschii tRNATyrCUA, indicating they are
poorer substrates for Escherichia coli synthetases.
[0239] Mutant AA2 also had very high affinity for Methanococcus
jannaschii TyrRS. Although this mutant tRNA could be stably
maintained in Escherichia coli, it slowed the growth rate of cells
for unknown reasons. This effect likely led to the emergence of
mutants AA3 and AA4, which both had a mutation outside of the
randomization region. Cells harboring AA3 or AA4 grew normally.
Nevertheless, AA3 and AA4 were relatively poor substrates for the
Methanococcus jannaschii TyrRS.
[0240] Four independent tRNAs were selected from two rounds of
negative and positive selections using the all-loop library. See
FIG. 13. All were poorer substrates for the Escherichia coli
synthetase than the parent Methanococcus jannaschii tRNATyrCUA, yet
were still efficiently charged by the Methanococcus jannaschii
TyrRS as shown by the in vivo .beta.-lactamase assay. See Table 2.
The IC.sub.50 value for cells expressing the best mutant, J17, was
12 .mu.g/ml ampicillin, which is even lower than that of cells with
the orthogonal tRNAGlnCUA derived from Saccharomyces cerevisiae
expressed (21 .mu.g/ml ampicillin). When J17 was coexpressed with
the Methanococcus jannaschii TyrRS, cells survived to an IC.sub.50
value of 436 .mu.g/ml ampicillin, providing a selection window
(ratio of IC.sub.50 value with TyrRS to IC50 value without TyrRS)
of 35-fold. In addition, the expression of all these mutant tRNAs
did not affect the growth of Escherichia coli cells.
2TABLE 2 In vivo .beta.-lactamase assay of selected suppressor
tRNAs IC.sub.50 (.mu.g/ml of ampicillin) Coexpressed with
Coexpressed with pBLAM pBLAM-JYRS Suppressor tRNA mj-tRNATyrCUA 56
1220 No tRNATyrCUA 10 10 Mutant tRNAs selected from anticodon-loop
library AA2 22 1420 AA3 10 110 AA4 12 135 Mutant tRNAs selected
from all-loop library Mutant tRNAs surviving both selections J15 30
845 J17 12 436 J18 20 632 J22 14 459 Mutant tRNAs surviving
negative selection only N11 11 16 N12 9 18 N13 10 12 N16 9 9
Plasmid pBLAM was used to express the .beta.-lactamase gene with an
amber codon at Ala184; plasmid pBLAM-JYRS expressed the amber
mutant and the TyrRS of Methanococcus jannaschii. Suppressor tRNAs
were encoded on pAC plasmid and cotransformed with pBLAM or
pBLAM-JYRS in the assay.
[0241] To confirm the properties of the selected suppressor tRNAs,
they were tested in another in vivo assay based on the suppression
of an amber codon in the chloramphenicol acetyltransferase (CAT)
gene. In contrast to .beta.-lactamase which is secreted into the
periplasm, CAT localizes in the cytoplasm. Moreover, ampicillin is
bacteriocidal while chloramphenicol is bacteriostatic. As shown in
Table 3 below, the selected suppressor tRNAs also were orthogonal
in the CAT assay, indicating their suitability for CAT
selections.
3TABLE 3 In vivo chloramphenicol acetyltransferase assay of
selected suppressor tRNAs IC.sub.50 (.mu.g/ml of chloramphenicol)
Suppressor tRNA pYC only pYC + pBK - JYRS mj-tRNATyrCUA 27 308 No
tRNATyrCUA 3 3 J15 11 297 J17 4 240 J18 6 284 J22 5 271 pYC
plasmids encoded the chloramphenicol acetyltransferase gene with an
amber codon at Asp112 and different suppressor tRNAs listed in the
left column of the table. pBK-JYRS was used to express the TyrRS of
Methanococcus jannaschii.
[0242] The in vivo complementation assay which is based on
suppression of an amber codon in the .beta.-lactamase gene was
carried out as described. See, e.g., Liu & Schultz, (1999),
supra; and, Wang, et al., (2000), supra. In the chloramphenicol
acetyltransferase (CAT) assay, an amber codon was substituted for
Asp112 in the CAT gene of pACYC184 to afford pACMD112TAG. See,
e.g., M. Pastrnak, T. J. Magliery, P. G. Schultz, A new orthogonal
suppressor tRNA/aminoacyl-tRNA synthetase pair for evolving an
organism with an expanded genetic code, Helv. Chim. Acta
83:2277-2286 (2000). The genes encoding the suppressor tRNAs under
the control of the lpp promoter and rrnC terminator were excised
from pAC plasmids with NcoI and AvaI, and inserted into the
pre-digested pACMD112TAG to afford plasmids pYC-JY, pYC-J15,
pYC-J17, pYC-J18, and pYC-J22, respectively. Plasmid pBK-JYRS, a
derivative of pBR322, was used to express the Methanococcus
jannaschii TyrRS under the control of the Escherichia coli GlnRS
promoter and terminator. The survival of Escherichia coli DH10B
cells transformed with pYC plasmid alone or cotransformed with pYC
and pBK-JYRS was titrated against a wide range of chloramphenicol
concentrations added to the growth media, and IC50 values were
interpolated from the curves.
[0243] For comparison, four colonies were randomly picked that
passed the negative selection only, and tested the tRNAs using the
in vivo complementation assay. All of them had very low IC.sub.50
values when transformed with pBLAM, indicating the negative
selection worked well. See Table 2. The IC.sub.50 values were also
low when cotransformed with pBLAM-JYRS, revealing that the positive
selection functions to delete tRNAs that cannot be charged by the
Methanococcus jannaschii TyrRS.
[0244] Analysis of the DNA sequences of the selected tRNAs yielded
a characteristic pattern of nucleotide substitutions. See FIG. 13.
tRNAs that passed both negative and positive selections all had C32
and T60 unchanged, while G37 was mutated to A, and T17a was mutated
to either A or G. Some semi-conserved changes included mutation of
A38 to either C or A; mutation of T45 to either T or A; mutation of
T47 to either G or T. Other mutations had no obvious common
pattern. Twenty (20) tRNAs that passed the negative selection only
were also sequenced, four of which are shown in FIG. 13, and found
they all lacked at least one of the common mutations listed
above.
[0245] The preferred nucleotides in the selected mutant suppressor
tRNAs can play the following roles: (i) they can function as
negative determinants for recognition by the Escherichia coli
synthetases; (ii) they can be identity elements for aminoacylation
by Methanococcus jannaschii TyrRS; or (iii) they can also optimize
the tRNA's interaction with Escherichia coli's translational
machinery so as to increase the suppression efficiency of the tRNA.
It is noteworthy that the G37A mutation was found in tRNAs selected
from both the anticodon-loop and all-loop library. This mutation is
consistent with previous studies that showing that adenine at
position 37 enhances amber suppression efficiency. See, e.g., M.
Yarus, Translational efficiency of transfer RNA's: Use of an
expanded anticodon, Science 218:646-652 (1982); D. Bradley, J. V.
Park, L. Soll, tRNA2Gln Su+2 mutants that increase amber
suppression, J. Bacteriol. 145:704-712 (1981); and, L. G. Kleina,
J. Masson, J. Normanly, J. Abelson, J. H. Miller, Construction of
Escherichia coli amber suppressor tRNA genes. II. Synthesis of
additional tRNA genes and improvement of suppressor efficiency, J.
Mol. Biol. 213:705-717 (1990). Fechter et al. recently reported
that the complete identity set for Methanococcus jannaschii tRNATyr
is six nucleotides (C1G72, A73, and anticodon G34U35A36). See P.
Fechter, J. Rudinger-Thirion, M. Tukalo, R. Gieg, Major tyrosine
identity determinants in Methanococcus jannaschii and Saccharomyces
cerevisiae tRNATyr are conserved but expressed differently, Eur. J.
Biochem. 268:761-767 (2001). The presence of C32 and T60 in all
selected mutant suppressors therefore is not required for
recognition by Methanococcus jannaschii TyrRS. All Escherichia coli
tRNAs have T at position 60 except four tRNAs which have C. See, M.
Sprinzl, C. Horn, M. Brown, A. Loudovitch, S. Steinberg,
Compilation of tRNA sequences and sequences of tRNA genes, Nucleic
Acids Res. 26:148-153 (1998). Based on the crystal structure of
yeast tRNAPhe, nucleotide 60 does not interact with other
nucleotides. See J. L. Sussman, S. R. Holbrook, R. W. Warrant, G.
M. Church, S. H. Kim, Crystal structure of yeast phenylalanine
transfer RNA. L Crystallographic refinement, J. Mol. Biol.
123:607-630 (1978). Thus, T60 may maintain the shape of the TC loop
for productive interaction with the Escherichia coli translational
machinery. The change of the TC loop structure may affect
translational fidelity, as the insertion of a nucleotide between
T60 and the conserved C61 enables a glycine tRNA to shift reading
frame. See, D. J. O'Mahony, B. H. Hims, S. Thompson, E. J. Murgola,
J. F. Atkins, Glycine tRNA mutants with normal anticodon loop size
cause 1 frameshifting, Proc. Natl. Acad. Sci. USA 86:7979-7983
(1989). The role of C32 is not obvious--position 32 in Escherichia
coli tRNAs includes T, C, and A, and two Escherichia coli tRNATyrs
do have C32. As for position 17a, only tRNAThr has an A at this
position.
[0246] All of the selected suppressor tRNAs are poorer substrates
for Escherichia coli synthetases relative to the Methanococcus
jannaschii tRNATyrCUA, resulting in less mischarging when
introduced into Escherichia coli. These tRNAs can also be stably
maintained in Escherichia coli without adverse effects on the
growth of host cells. Moreover, they can still be charged
efficiently by Methanococcus jannaschii TyrRS. All these properties
make the mutant suppressor tRNA together with the Methanococcus
jannaschii TyrRS a robust orthogonal tRNA-synthetase pair for the
selective incorporation of unnatural amino acids into proteins in
vivo. The J17 mutant suppressor tRNA and an engineered mutant TyrRS
has been used to deliver O-methyl-L-tyrosine in response to a TAG
codon with a fidelity rivaling that of the common 20 amino acids.
See, L. Wang, A. Brock, B. Herberich, P. G. Schultz, Expanding the
genetic code of Escherichia coli, Science, 292:498-500 (2001).
Example 2
Mutating TyrRS so that it Charges the mutRNA Tyr/CUA with an
Unnatural Amino Acid, O-methyl-L-tyrosine
[0247] A unique transfer RNA (tRNA)-aminoacyl tRNA synthetase pair
has been generated that expands the number of genetically encoded
amino acids in Escherichia coli. When introduced into Escherichia
coli, this pair leads to the in vivo incorporation of the synthetic
amino acid O-methyl-L-tyrosine, added exogenously to the growth
medium, into protein in response to an amber nonsense codon. The
fidelity of translation is greater than 99%, as determined by
analysis of dihydrofolate reductase containing the unnatural amino
acid. This approach provides a general method for increasing the
genetic repertoire of living cells to include a variety of amino
acids with novel structural, chemical and physical properties not
found in the common twenty amino acids.
[0248] An orthogonal tRNA/synthetase pair in Escherichia coli can
be generated by importing a pair from a different organism, if
cross-species aminoacylation is inefficient, and, optionally, the
anticodon loop is not a key determinant of synthetase recognition.
One such candidate pair is the tyrosyl tRNA/synthetase pair of
Methanococcus jannaschii (Methanococcus jannaschii), an
archaebacterium whose tRNATyr identity elements differ from those
of Escherichia coli tRNA.sup.Tyr (in particular, the first base
pair of the acceptor stem is GC in Escherichia coli and CG in
Methanococcus jannaschii), and whose tyrosyl synthetase (TyrRS) has
only a minimalist anticodon loop binding domain. See, e.g., B. A.
Steer, & P. Schimmel, J. Biol. Chem. 274:35601-6 (1999). In
addition, the Methanococcus jannaschii TyrRS does not have an
editing mechanism, see, e.g., Jakubowski & Goldman, Microbiol.
Rev., 56:412 (1992), and therefore should not proofread an
unnatural amino acid ligated to the tRNA. The Methanococcus
jannaschii TyrRS efficiently aminoacylates an amber suppressor tRNA
derived from its cognate tRNATyr, see, e.g., Wang, et al., (2000 J.
Am. Chem. Soc., supra., but does not aminoacylate Escherichia coli
tRNAs, see, e.g., Steer & Schimmel, (1999), supra. Moreover,
the Methanococcus jannaschii tRNA.sub.CUA.sup.Tyr is a poor
substrate for the Escherichia coli synthetases but functions
efficiently in protein translation in Escherichia coli. See, e.g.,
Wang, et al., (2000 J. Am. Chem. Soc., supra.
[0249] To further reduce recognition of the orthogonal tRNA,
Methanococcus jannaschii tRNA.sub.CUA.sup.Tyr, by Escherichia coli
synthetases, eleven nucleotides of the tRNA that do not interact
directly with the Methanococcus jannaschii TyrRS(C16, C17, U17a,
U20, C32, G37, A38, U45, U47, A59 and U60) were randomly mutated to
generate a suppressor tRNA library. This tRNA library was passed
through a negative selection (e.g., suppression of amber mutations
in a toxic reporter gene, e.g., barnase gene), which removes tRNAs
that are aminoacylated by Escherichia coli synthetases, and then a
positive selection for tRNAs that are efficiently aminoacylated by
Methanococcus jannaschii TyrRS (e.g., suppression of amber
mutations in a reporter gene, e.g., .beta.-lactamase gene).
[0250] The orthogonal nature of the resulting suppressor tRNAs was
tested by an in vivo complementation assay, which is based on
suppression of an amber stop codon at a nonessential position
(e.g., Ala184) of a reporter gene on a vector, e.g., the TEM-1
.beta.-lactamase gene carried on plasmid pBLAM. Aminoacylation of a
transformed suppressor tRNA by any endogenous Escherichia coli
synthetase results in cell growth in the presence of ampicillin.
Escherichia coli transformed with Methanococcus jannaschii
tRNA.sub.CUA.sup.Tyr and the reporter construct, pBLAM, survive at
55 .mu.g/mL ampicillin. When the best mutant suppressor tRNA
(mtRNA.sub.CUA.sup.Tyr) selected from the library was expressed,
cells survived at only 12 .mu.g/mL ampicillin; similar values are
obtained in the absence of any suppressor tRNA. The mutant
suppressor tRNA contained the following nucleotide substitutions:
C17A, U17aG, U20C, G37A, and U47G. When the Methanococcus
jannaschii TyrRS is coexpressed with this mtRNA.sub.CUA.sup.Tyr,
cells survive at 440 .mu.g/mL ampicillin. Thus, the
mtRNA.sub.CUA.sup.Tyr is a poorer substrate for the endogenous
synthetases than the Methanococcus jannaschii tRNA.sub.CUA.sup.tyr
but is still aminoacylated efficiently by the Methanococcus
jannaschii TyrRS.
[0251] To alter the amino acid specificity of the orthogonal TyrRS
so that it charges the mtRNA.sub.CUA.sup.Tyr with a desired
unnatural amino acid, a library of TyrRS mutants was generated and
screened. Based on the crystal structure of the homologous TyrRS
from Bacillus stearothermophilus, see, e.g., P. Brick, T. N. Bhat,
D. M. Blow, J. Mol. Biol., 208:83 (1988), five residues
(Tyr.sup.32, Glu.sup.107, Asp.sup.158, Ile.sup.159 and Leu.sup.162)
in the active site of Methanococcus jannaschii TyrRS which are
within 6.5 .ANG. of the para position of the aryl ring of bound
tyrosine were mutated. See, FIG. 14. These residues were all
initially mutated to alanine, and the resulting inactive Alas TyrRS
was used as a template for polymerase chain reaction (PCR) random
mutagenesis with doped oligonucleotides.
[0252] For example, the TyrRS gene was expressed under the control
of Escherichia coli GlnRS promoter and terminator in plasmid
pBK-JYRS, a pBR322 derived plasmid with kanamycin resistance.
Residues Tyr.sup.32, Glu.sup.107, Asp.sup.158, Ile.sup.159 and
Leu.sup.162 were substituted with Ala by site-directed mutagenesis
to provide plasmid pBK-JYA5. Eight (8) oligonucleotides with NNK
(N=A+T+G+C and K=G+T, and M=C+A), e.g., oligonucleotides LW157
5'-GGAATTCCATATGGACGAATTTGAAATG-3', LW164 5'-GTATTT
TACCACTTGGTTCAAAACCTATMNNAGCAGATTTTTCATCTTTTTTTCATCTTT
TTTTAAAAC-3', LW159 5'-TAGGTTTTGAACCAAGTGGTAAAATAC-3', LW165
5'-CATTCAGTGTATAATCCTTATCAAGCTGGAAMNNACTTCCATAA
ACATATTTTGCCTTAAC-3', LW161 5'-TCCAGCTTGATAAGGATTATACA CTGAATG-3',
LW167 5'-CATCCCTCCAACTGCAACATCAACGCCMNNATA
ATGMNNNATTAACCTGCATTATTGGATAGATAAC-3- ', LW163 5'-GCGT
TGATGTTGCAGTTGGAGGGATG-3', and LW105 5'-AAACTGCAGTTATAAT
CTCTTTCTAATTGGCTC-3' (Operon, CA) at the mutation sites were used
for PCR amplification of the Ala.sub.5 TyrRS mutant (pBK-JYA5) and
ligated back into the NdeI-PstI-digested pBK-JYA5 to afford the
TyrRS library. The ligated vectors were transformed into
Escherichia coli DH10B competent cells to yield a library of
1.6.times.10.sup.9 colony forming unit (cfu). The TyrRS genes from
40 randomly picked colonies were sequenced to confirm that there
was no base bias at the randomized NNK positions and no other
unexpected mutations. The library was amplified by maxiprep, and
supercoiled DNA was used to transform the selection strain
pYC-J17.
[0253] A positive selection was then applied to the library of
mutated orthogonal-TyrRS that is based on suppression of an amber
stop codon at a nonessential position (e.g., Asp112) in the
chloramphenicol acetyltransferase (CAT) gene. See, e.g., M.
Pastrnak, T. J. Magliery, P. G. Schultz, Helv. Chim. Acta, 83:2277
(2000). Cells transformed with the mutant TyrRS library and
mtRNA.sub.CUA.sup.Tyr gene were grown in media containing the
unnatural amino acid and selected for their survival in the
presence of various concentrations of chloramphenicol. If a mutant
TyrRS charges the orthogonal mtRNA.sub.CUA.sup.Tyr with any amino
acid, either natural or unnatural, the cell produces CAT and
survives. The surviving cells were then grown in the presence of
chloramphenicol and in the absence of the unnatural amino acid.
Those cells that did not survive, e.g., which encode mutant TyrRS's
that charge the orthogonal mtRNA.sub.CUA.sup.Tyr with an unnatural
amino acid, were isolated from a replica plate supplemented with
the unnatural amino acid. The mutant TyrRS genes were isolated from
these cells, recombined in vitro by DNA shuffling, and transformed
back into Escherichia coli for further rounds of selection with
increasing concentrations of chloramphenicol.
[0254] A tyrosine analogue with the para hydroxyl group substituted
with the methoxy group was used in the selection. Optionally, other
tyrosine analogues can also be used in selection, e.g., tyrosine
analogues with different functional groups at the para position of
the aryl ring (acetyl, amino, carboxyl, isopropyl, methyl, O-methyl
and nitro, etc.). For example, the gene encoding
mtRNA.sub.CUA.sup.Tyr was expressed in Escherichia coli DH10B cells
under the control of the lpp promoter and rrnC terminator in
plasmid pYC-J17, a pACYC184 derivative that also encodes the
Asp.sub.112 TAG CAT mutant. Supercoiled DNA encoding the TyrRS
library was transformed into Escherichia coli DH10B competent cells
containing pYC-J17 to yield a library of size greater than
3.times.10.sup.9 cfu, ensuring complete coverage of the original
library. Cells were then plated on minimal media plates containing
1% glycerol and 0.3 mM leucine (GMML) with 17 .mu.g/mL tetracycline
(Tet), 25 .mu.g/mL kanamycin (Kan), 50 .mu.g/mL of chloramphenicol
(Cm), and 1 mM unnatural amino acid. After incubation at 37.degree.
C. for 44 hours, colonies on plates supplied with
O-methyl-L-tyrosine were pooled, plasmids were isolated and
retransformed into Escherichia coli DH10B competent cells
containing pYC-J17, and the transformed cells were positively
selected on 50 .mu.g/mL of Cm. Colonies (96) were individually
picked from the plate, diluted into 100 .mu.L of liquid GMML media,
and streaked onto two sets of Kan/Tet GMML plates with various
concentration of Cm. No O-methyl-L-tyrosine was added to plate set
1 and the concentration of Cm was varied from 10-25 .mu.g/mL; plate
set 2 contained 1 mM O-methyl-L-tyrosine and 50 .mu.g/mL of Cm.
Replicates of colonies that did not grow on 15 .mu.g/mL of Cm in
plate set 1 were picked from plate set 2. Plasmids containing the
TyrRS gene were purified and recombined in vitro by DNA shuffling
using Stemmer's protocol with the exception of 10 mM Mn2+ instead
of Mg2+ in the fragmentation reaction. See, W. P. C. Stemmer,
Nature 370, 389-91 (1994); and, I. A. Lorimer, I. Pastan, Nucleic
Acids Res. 23, 3067-8 (1995). The library was then religated into
predigested pBK-JYA5 vector to afford a second generation TyrRS
library with a typical size of 8.times.10.sup.8 to 3.times.10.sup.9
cfu. Thirty randomly selected members from the library were
sequenced. The mutagenic rate introduced by DNA shuffling was
0.35%. This library was transformed into the selection strain for
the next round of selection followed by shuffling. The
concentration of Cm in the positive selection and in plate set 2
was raised to 80 .mu.g/mL for the second round and 120 .mu.g/mL for
the third round; the concentration of Cm in plate set 1 was
unchanged. After three rounds of DNA shuffling, colonies began to
grow on 20-25 .mu.g/mL Cm in plate set 1, indicating that the TyrRS
mutants were accepting natural amino acids as substrates.
Therefore, the best clone selected after two rounds of DNA
shuffling was characterized in detail.
[0255] Two rounds of selection and DNA shuffling were carried out
and a clone was evolved whose survival in chloramphenicol was
dependent on the addition of 1 mM O-methyl-L-tyrosine to the growth
media. In the absence of O-methyl-L-tyrosine, cells harboring the
mutant TyrRS were not viable on minimal media plates containing 1%
glycerol, 0.3 mM leucine (GMML), and 15 .mu.g/mL of
chloramphenicol. Cells were able to grow on GMML plates with 125
.mu.g/mL chloramphenicol in the presence of 1 mM
O-methyl-L-tyrosine. Similar results were obtained in liquid GMML.
As a control, cells with the mtRNA.sub.CUA.sup.Tyr and the inactive
Ala.sub.5 TyrRS did not survive at the lowest concentration of
chloramphenicol used, either in the presence or absence of 1 mM
O-methyl-L-tyrosine. See FIG. 14. Addition of 1 mM
O-methyl-L-tyrosine itself does not significantly affect the growth
rate of Escherichia coli.
[0256] Analysis of the sequence of the mutant TyrRS that charges
the mtRNA.sub.CUA.sup.Tyr with O-methyl-L-tyrosine revealed the
following mutations: Tyr.sup.32.fwdarw.Gln.sup.32,
Asp.sup.158.fwdarw.Ala.sup.158, Glu.sup.107.fwdarw.Thr.sup.107, and
Leu.sup.162.fwdarw.Pro.sup.162. See FIG. 14. Based on the x-ray
crystal structure of the homologous B. stearothermophilus TyrRS,
the loss of the hydrogen-bonding network between Tyr.sup.32,
Asp.sup.158 and substrate tyrosine can disfavor binding of tyrosine
to the mutant TyrRS. Indeed, mutation of Asp.sup.176 (which
corresponds to Asp.sup.158 in Methanococcus jannaschii) of B.
stearothernophilus TyrRS yields inactive enzyme. See, e.g., G. D.
P. Gray, H. W. Duckworth, A. R. Fernst, FEBS Lett. 318:167 (1993).
At the same time, the Asp.sup.158.fwdarw.Ala.sup.158 and
Leu.sup.162.fwdarw.Pro.- sup.162 mutations create a hydrophobic
pocket that allows the methyl group of O-methyl-L-tyrosine to
extend further into the substrate-binding cavity. Other important
catalytic residues in the active site, which bind to the ribose or
the phosphate group of the adenylate, were unchanged after two
rounds of DNA shuffling.
[0257] Kinetics of adenylate formation of O-methyl-L-tyrosine and
tyrosine with adenosine triphosphate (ATP) catalyzed by the mutant
TyrRS were analyzed in vitro using a pyrophosphate-exchange assay
at 37.degree. C. For example, the mutant TyrRS gene with six
histidines at its C-terminus was cloned into plasmid pQE-60
(Qiagen, CA) to generate plasmid pQE-mJYRS. Protein was purified by
immobilized metal affinity chromatography according to
manufacture's protocol (Qiagen, CA). Pyrophosphate (PPi) exchange
was carried out at 37.degree. C. in a reaction mixture containing
100 mM Tris HCl (pH7.5), 10 mM KF, 5 mM MgCl2, 2 mM ATP, 2 mM
NaPPi, 0.1 mg/mL bovine serum albumin, approximately 0.01
.mu.Ci/.mu.L [.sup.32P]NaPPi, and various concentrations of
tyrosine or O-methyl-L-tyrosine. Reactions were initiated with the
addition of the purified mutant TyrRS, and aliquots were
periodically taken and quenched with 0.2 M NaPPi, 7% perchloric
acid, and 2% activated charcoal. The charcoal was filtered and
washed with 10 mM NaPPi (pH2), then measured by scintillation
counting to determine the .sup.32P levels in charcoal-adsorbed ATP.
Values of k.sub.cat and K.sub.m were calculated by direct fitting
of the Michaelis-Menten equation using nonlinear regression
analysis.
[0258] The Michaelis constant (K.sub.m) for tyrosine (5833+/-902
.mu.M) is approximately 13-fold higher than that for
O-methyl-L-tyrosine (443+/-93 .mu.M), and the catalytic rate
constant (k.sub.cat) for tyrosine (1.8+/-0.2.times.10.sup.-3
s.sup.-1) is eightfold less than that for O-methyl-L-tyrosine
(14+/-1.times.10.sup.-3 s.sup.-1). Thus, the value of
k.sub.cat/K.sub.m of the mutant TyrRS for O-methyl-L-tyrosine is
about 100-fold higher than that of tyrosine. The physiological
concentration of tyrosine in Escherichia coli is about 80 .mu.M,
which is far below K.sub.m value (5833 .mu.M) of the mutant TyrRS
for tyrosine. Presumably, the concentration of O-methyl-L-tyrosine
in cells is comparable or greater than the K.sub.m (443 .mu.M).
[0259] This example shows that it is possible to augment the
protein biosynthetic machinery of Escherichia coli to accommodate
additional genetically encoded amino acids. The ability to
introduce novel amino acids into proteins directly in living cells
will provide new tools for studies of protein and cellular function
and can lead to generation of proteins with enhanced properties
compared to a naturally occurring protein. The methods described
here can be applied to other amino acids with novel spectroscopic,
chemical, structural or the like properties. The Escherichia coli
ribosome has been shown to be able to incorporate amino acids with
a wide array of side chains into proteins using in vitro protein
synthesis. See, e.g., C. J. Noren, S. J. Anthony-Cahill, M. C.
Griffith, P. G. Schultz, Science 244, 182-8 (1989). Additional
orthogonal tRNA/synthetase pairs, see, e.g., D. R. Liu, P. G.
Schultz, Proc. Natl. Acad. Sci. USA 96,4780-5 (1999); and, A. K.
Kowal, C. Kohrer, U. L., RajBhandary, Proc. Natl. Acad. Sci,
U.S.A., 98:2268 (2001), as well as four base codons, see, e.g., T.
J. Magliery, J. C. Anderson, P. G. Schultz, J. Mol. Biol. 307:755
(2001); and, B. Moore, B. C. Persson, C. C. Nelson, R. F.
Gesteland, J. F. Atkins, J. Mol. Biol., 298:195 (2000), and other
selector codons described herein, can further expand the number and
scope of amino acids that can be incorporated. Orthogonal pairs for
eukaryotic cells can also be generated by the methods provided
herein.
[0260] See also corresponding patent application "In vivo
Incorporation of Unnatural Amino Acids" attorney docket number
54-000120PC/US which is incorporated herein by reference. This
application describes an example of the generation of an
O-methyl-L-tyrosine mutant of dihydrofolate reductase (DHFR) using
the above-described system.
Example 3
Mutating TyrRS so that it Charges the mutRNA Tyr/CUA with an
Unnatural Amino Acid, L-3-(2-Napthyl)alanine
[0261] This example provides another orthogonal pair that can be
used to incorporate a second unnatural amino acid,
L-3-(2-Napthyl)alanine into proteins in an organism, e.g.,
Escherichia coli. An example of the methods used to generate the
orthogonal pair that incorporates the unnatural amino acid into
proteins is described below. More details describing the
incorporation of the unnatural amino acid into a protein can be
found in corresponding patent application "In vivo incorporation of
unnatural amino acid" attorney docket number 54-000120PC/US
incorporated herein by reference.
[0262] An amber stop codon and its corresponding orthogonal amber
suppressor tRNA, mu tRNA.sub.CUA.sup.Tyr, were selected to encode
an unnatural amino acid. As described above, and see Wang &
Schultz, Chem. Biol. 8:883-890 (2001). The Methanococcus jannaschii
tyrosyl-tRNA synthetase (TyrRS) was used as the starting point for
the generation of an orthogonal synthetase with unnatural amino
acid specificity. This TyrRS does not aminoacylate any endogenous
Escherichia coli tRNAs, see, e.g., Steer & Schimmel, J. Biol.
Chem., 274:35601-35606 (1999), but aminoacylates the mu
tRNA.sub.CUA.sup.Tyr with tyrosine. See, e.g., Wang, Magliery, Liu,
Schultz, J. Am. Chem. Soc., 122:5010-5011 (2000).
L-3-(2-naphthyl)-alanine was chosen for this study since it
represents a significant structural perturbation from tyrosine and
may have novel packing properties. To change the amino acid
specificity of the TyrRS so that it charges the mu
tRNA.sub.CUA.sup.Tyr with L-3-(2-naphthyl)-alanine and not any
common 20 amino acids, a library of Methanococcus jannaschii TyrRS
mutants was generated and screened. On the basis of an analysis of
the crystal structure of the homologous TyrRS from Bacillus
stearothermophilus, see, Brick, Bhat, Blow, J. Mol. Biol.,
208:83-98 (1989), five residues (Tyr.sup.32, Asp.sup.158,
Ile.sup.159, Lue.sup.162, and Ala.sup.167) in the active site of
Methanococcus jannaschii TyrRS that are within 7 .ANG. of the para
position of the aryl ring of tyrosine were mutated. See FIG. 15. No
synthetases specific for L-3-(2-naphthyl)alanine were selected from
the mutant TyrRS library reported in Wang, Brock, Herberich,
Schultz, Science, 292:498-500 (2001). To reduce the wild-type
synthetase contamination in the following selection, these residues
(except Ala.sup.167) were first all mutated to alanine. The
resulting inactive Ala.sub.5 TyrRS gene was used as a template for
polymerase chain reaction (PCR) random mutagenesis with
oligonucleotides bearing random mutations at the corresponding
sites.
[0263] The mutant TyrRS library was first passed through a positive
selection based on suppression of an amber stop codon at a
nonessential position (Asp.sup.112) in the chloramphenicol
acetyltransferase (CAT) gene. Cells transformed with the mutant
TyrRS library and the mu tRNA.sub.CUA.sup.Tyr gene were grown in
minimal media containing 1 mM L-3-(2-naphthyl)-alanine and 80
.mu.g/mL chloramphenicol. Cells can survive only if a mutant TyrRS
aminoacylates the mu tRNA.sub.CUA.sup.Tyr with either natural amino
acids or L-3-(2-naphthyl)-alanine. The surviving cells were then
grown in the presence of chloramphenicol and the absence of the
unnatural amino acid. Those cells that did not survive must encode
a mutant TyrRS that charges the mu tRNA.sub.CUA.sup.Tyr with
L-3-(2-naphthyl)-alanine, and were picked from a replica plate
supplied with the unnatural amino acid. After three rounds of
positive selection followed by a negative screen, four TyrRS's were
characterized using an in vivo assay based on the suppression of
the Asp.sup.112TAG codon in the CAT gene.
4TABLE 4 In vivo chloramphenicol acetyltransferase assay of mutant
TyrRS..sup.a IC.sub.50 (.mu.g/mL of chloramphenicol) No
L-3-(2-naphthyl)-Ala Add L-3-(2-naphthyl)-Ala Mutant TyrRS no TyrRS
4 4 wt TyrRS 240 240 After selection S1-TyrRS 30 120 S2-TyrRS 30
120 S3-TyrRS 25 110 S4-TyrRS 35 100 After DNA shuffling SS12-TyrRS
9 150 .sup.aA pYC-J17 plasmid was used to express the mu
.sub.tRNAS.sub..sub.CUA.sup.Tyr gene and tne chloramphenicol
acetyltransferase gene with an amber stop codon at Asp112. A pBK
plasmid was used to express TyrRS, and was cotransformed with
pYC-J17 into Escherichia coli DH10B. Cell survival on GMML plates
was titrated in the presence of different concentrations of
chloramphenicol.
[0264] In the absence of L-3-(2-naphthyl)-alanine, cells expressing
the selected TyrRS and the mu tRNA.sub.CUA.sup.Tyr survived in 25
to 35 .mu.g/mL chloramphenicol on minimal media plates containing
1% glycerol and 0.3 mM leucine (GMML plate); in the presence of
L-3-(2-naphthyl)-alanine, cells survived in 100 to 120 .mu.g/mL
chloramphenicol on GMML plates. Compared to the IC.sub.50 value in
the absence of any TyrRS (4 .mu.g/1 mL chloramphenicol), these
results indicate that the selected TyrRS's accept
L-3-(2-naphthyl)-alanine, but also still charge natural amino acids
to some degree. See Table 4 above.
[0265] To further reduce the activity of the mutant TyrRS toward
natural amino acids, one round of DNA shuffling was carried out
using the above four mutant genes as templates. The resulting
mutant TyrRS library was passed through two additional rounds of
positive selections and negative screens. One mutant
TyrRS(SS12-TyrRS) was evolved, whose activity for natural amino
acids was greatly reduced (IC.sub.50=9 .mu.g/mL chloramphenicol)
while its activity toward L-3-(2-naphthyl)-alanine was enhanced
(IC.sub.50=150 .mu.g/mL chloramphenicol). See Table 4.
[0266] The evolved SS12-TyrRS has the following mutations:
Tyr.sup.32.fwdarw.Leu.sup.32, Asp.sup.158.fwdarw.Pro.sup.158,
Ile.sup.159.fwdarw.Ala.sup.159, Leu.sup.162.fwdarw.Gln.sup.162, and
Ala.sup.167.fwdarw.Val.sup.167. See FIG. 15. Based on the crystal
structure of the homologous B. stearothermophilus TyrRS, the
mutations of Tyr.sup.32.fwdarw.Leu.sup.32 and
Asp.sup.158.fwdarw.Pro.sup.158 can result in the loss of hydrogen
bonds between Tyr.sup.32, Asp.sup.158, and the native substrate
tyrosine, thus disfavoring the binding of tyrosine to SS12-TyrRS.
Most residues are mutated to amino acids with hydrophobic side
chains, which are expected to favor binding of
L-3-(2-naphthyl)-alanine. The crystal structure of the wild-type
Methanococcus jannaschii TyrRS and the evolved SS12-TyrRS can be
determined by available methods.
[0267] The mu tRNA.sub.CUA.sup.Tyr/SS12-TyrRS pair was capable of
selectively inserting L-3-(2-naphthyl)-alanine into proteins in
response to the amber codon with fidelity rivaling that of the
natural amino acids based on cell growth, protein expression and
mass spectrometry examples described herein and in corresponding
application "In vivo incorporation of unnatural amino acids"
attorney docket number 54-000120PC/US. See also, Wang, Brock, and
Schultz, Adding L-3-(2-Naphthyl)alanine to the genetic code of E.
coli, J. Am. Chem Soc., (2002) 124(9):1836-7. This result, which
involves an amino acid that is structurally distinct from tyrosine,
confirms that the methods described herein are generalizable to a
variety of unnatural amino acids.
Example 4
Mutating TyrRS so that it Charges the mutRNA Tyr/CUA and Screening
for the Mutated TyrRS with the Desired Properties by Other Methods,
e.g., FACs and Phage Display and Panning
[0268] Orthogonal pairs can also be selected by using reporter
genes and proteins as described above, along with in vivo FACS
screening, antibody detection, in vitro phage display and panning,
or the like. See, Wang & Schultz, Expanding the genetic code,
Chem. Commun., 1:1-11 (2002).
[0269] For example, a general fluorescence-activated cell sorting
(FACS) based screen has been developed with, e.g., green
fluorescent protein (GFP) as the reporter, to screen for
synthetases. See FIG. 16, Panel A, and Panel B Synthetase activity
is reported by suppression of the selector codon, e.g., an amber
stop codon (TAG) within T7 RNA polymerase, which drives the
expression of GFP. See, e.g., FIG. 26 for another example of
selection/screening methods of the invention. Only when the amber
codons are suppressed can cells produce functional T7 RNA
polymerase and express GFP, rendering cells fluorescent. In the
positive screen, fluorescent cells are collected which encode
active synthetases charging the orthogonal tRNA with either natural
or unnatural amino acids. The selected cells are then diluted and
grown in the absence of the unnatural amino acid, and then sorted
by FACS for cells without fluorescence, e.g., that express
synthetases with specificities for unnatural amino acids only. FIG.
17, Panel A, Panel B Panel C and Panel D illustrates suppression of
a selector codon, e.g., an amber codon, using glutamine synthetase.
By setting the collection threshold of the fluorescence intensity,
the stringency of both positive and negative screen can be
conveniently controlled.
[0270] A direct positive selection specific for a particular
unnatural amino acid has also been developed which exploits the
high affinity of a monoclonal antibody for an unnatural amino acid
displayed on a phage surface. See FIG. 18. See, M. Pastrnak and P.
G. Schultz, Bioorg. Med. Chem., 9:2373 (2001). For example, a C3
peptide with an amber mutation is fused to the N-terminus of VSCM13
phage coat protein pIII, such that phage production requires
suppression of the amber stop codon. Cells harboring a phagemid
that expresses an orthogonal suppressor tRNA and a synthetase
library are infected with the C3TAG phage. An active synthetase
results in suppression of C3TAG and display of its cognate amino
acid on the phage surface. The phage pool is then incubated with
immobilized monoclonal antibodies directed against the unnatural
amino acid to isolate only those phage carrying the synthetase
specific for the unnatural amino acid. In a simulated selection,
phage displaying Asp were enriched over 300-fold from a pool of
phage displaying Asn using antibodies raised against the
Asp-containing epitope.
[0271] Several in vitro screen methods can also be used. In one
such method, a library of mutant synthetases is displayed on the
phage, and the phage particles are panned against immobilized
aminoalkyl adenylate analogs of the aminoacyl adenylate
intermediate. See FIG. 19. For example, Methanococcus jannaschii
TyrRS was fused to the pIII coat protein of M13 phage. This phage
was enriched 1000-fold over a control phage displaying an unrelated
antibody after panning against the aminoalkyl adenylate analog of
tyrosyl adenylate. Given that only 0.1 to 1% of the starting TyrRS
phage population displays the TyrRS protein, the actual enrichment
factor can be as high as 10.sup.5 to 10.sup.6.
Example 5
Generating an Archaeal leucyl-tRNA Synthetase Pair
[0272] A leucyl-tRNA synthetase from an archaebacterium,
Methanobacterium thermoautotrophicum, was identified that can
aminoacylate amber and frameshift suppressor tRNAs derived from
archaeal leucyl tRNAs, but does not aminoacylate any tRNAs native
to Escherichia coli. Using a selection strategy described in the
present invention, highly active tRNA substrates were identified
that are selectively charged by the synthetase. Mutant libraries of
synthetases can be generated and selected for that are capable of
selectively charging unnatural amino acids.
[0273] .beta.-lactamase reporter genes were constructed with amber
codons and suppressor tRNAs derived from five different archael
leucyl tRNAs for which the anticodon was replaced with a CUA
anticodon to make amber suppressor tRNAs. Seven different leucyl
tRNA synthetases were cloned and were cotransformed with reporter
constructs. Three synthetases gave higher levels of survival on
ampicillin in the presence of the synthetase than controls lacking
synthetase, and these systems were examined further. See, FIG.
20.
[0274] The next step involved determination of a synthetase that
charges the suppressor tRNA without interacting with host tRNA. The
two chosen systems, Methanobacterium thermoautotrophicum and
Methanococcus jannaschii were expressed, and aminoacylation was
performed in vitro on purified tRNA from Halobacterium as a
positive control, and for Escherichia coli total tRNA. It was found
that the Methanococcus jannaschii synthetase was able to
effectively charge Escherichia coli tRNA, but the Methanobacterium
thermoautotrophicum synthetase was specific towards the
Halobacterium tRNA.
[0275] Further improvements were made to increase the efficiency of
the suppression system. The A.sup.37 site of the anticodon loop was
a G.sup.37 in the leucyl tRNA synthetases. This mutation has been
shown to be a negative determinant against aminoacylation by
non-cognate synthetases in various eukaryotic cells and
Halobacterium, and also a positive determinate for aminoacylation
in yeast, but not in Halobacterium. A.sup.37 was also shown to be a
key requirement for efficient suppression. The anticodon loop was
randomly mutagenized and selected for more efficient suppression.
Mutating G.sup.37 to A, resulted in a more efficient suppressor,
which could suppress 20 fold higher concentrations of ampicillin
compared to the un-mutated version. See, FIG. 21.
[0276] To improve the tRNA so that is not preferentially charged by
other synthetases in Escherichia coli, the acceptor stem of the
tRNA was randomly mutagenized. A positive/negative selection was
used to identify tRNAs that would not be charged in the absence of
Methanobacterium thermoautotrophicum RS.
[0277] Amongst the selected mutated tRNAs observed, all conserved
the discriminator base, A.sup.73, which has been shown in all
previous systems to be a critical positive determinate for leucyl
aminoacylation. Also conserved was a C.sup.3:G.sup.70 base pair
amongst all hits that had improved orthogonality. The best mutant
tRNA observed gave about a 3-fold decrease in aminoacylation
without synthetase and actually an increase in suppression in the
presence of Methanobacterium thermoautotrophicum RS.
[0278] Variants were also made that could suppress four-base codons
instead of, e.g., three base codons. Four base codons offer the
possibility of decoding the genetic code four bases at a time, for
which 256 things could be encoded rather than 3 at a time, where
only 64 amino acids can be encoded. The difficulty with using
four-base codons is that they require expansion of the anticodon
loop for the tRNA, a perturbation which most systems are unlikely
to accept. However, a first generation AGGA suppressor for the
leucyl system was identified. This was generated by randomly
mutagenizing the anticodon loop with 8 bases and performing
selection with an AGGA-.beta.-lactamase reporter system. See FIG.
22.
[0279] The editing mechanism of the synthetase was also mutated to
eliminate the editing function. The leucyl system, like several
other synthetases has (at least) two active sites. One site
performs activation of the amino acid with ATP to form an enzyme
bound aminoacyl adenylate in complex with the synthetase, and then
transfer of the amino acid onto the 3' terminus of the tRNA. A
second site, however, is able to hydrolyze the amino acid from the
tRNA if it is not leucine. The leucine system is known to perform
this post-transfer editing function for methionine and isoleucine,
and it optionally does this to unnatural amino acids as well.
[0280] Initially, the editing domain was deleted. The editing
domain was replaced with a library of 6 tandem random amino acids.
A positive selection was used, which was based on suppression of a
stop codon in .beta.-lactamase. Many functional synthetases were
obtained, but upon trying to purify the synthetases, no material in
any cases could be detected, and all of these synthetases displayed
a temperature sensitive phenotype suggesting that the deletion of
the editing domain resulted in a less stable protein.
[0281] Next, point mutations were made in the editing domain. The
catalytic core of the editing domain is well conserved across
species and even for different amino acids, at least for the family
of branched chain amino acids. Several of these conserved sites
have previously been mutated, for example a T.fwdarw.P mutation,
and found to knock out editing function. Mutants of
Methanobacterium thermoautotrophicum RS were constructed that were
similar to several known mutants, and also a 20 member NNK library
derived from T214 was made. Proteins were expressed and examined in
vitro for aminoacylation with leucine and methionine. None of the
previously identified mutations were transferable to our system,
but a desirable mutation was identified from the T214 library. Two
mutants were identified that were capable of charging with leucine,
T214S and T214Q. Of these mutations, only T214Q was capable of
charging methionine. The T214S mutant apparently retains the
ability to edit out methionine whereas the Gln mutant has lost this
function.
[0282] A library was then designed based on the crystal structure
that has been solved for the Thermus thermophilus leucyl
synthetase. The leucine side chain of the leucine aminoalkyl
adenylate analog adenosine inhibitor was bound in the active site.
Six sites surrounding the leucine side chain-binding pocket were
replaced with randomized amino acids to create a larger library.
The synthetases from this library can then be screened, e.g., by
performing positive/negative double sieve selections, to identify
synthetases capable of charging unnatural amino acids
selectively.
Example 6
Identification of tRNAs that Efficiently Suppress Four-Base
Codons
[0283] A combinatorial approach was used to identify mutated tRNAs
that efficiently suppress four-base codons. See, T. J. Magliery, J.
C. Anderson and P. G. Schultz, J. Mol. Biol., 307:755 (2001). A
reporter library was constructed in which a serine codon in the
.beta.-lactamase gene was replaced by four random nucleotides. A
mutated tRNA, e.g., suppressor tRNA, suppressor library was then
generated that consists of derivatives of Escherichia coli with the
anticodon loop (7 nt) replaced with eight or nine random
nucleotides. When these two libraries are crossed, an appropriate
frameshift suppressor tRNA that decodes the four-base sequence as a
single codon results in translation of full-length
.beta.-lactamase, rendering the cells resistant to ampicillin.
Survival at higher concentrations of ampicillin indicates that the
corresponding tRNA has higher suppression efficiency for the
four-base codon. Using this selection, four quadruplet codons AGGA,
CUAG, UAGA, and CCCU and their cognate suppressor tRNAs were
identified that decode only the canonicai four-base codon with
efficiencies close to that of natural triplet codon suppressors.
Novel five- and six-base codon suppressors have also been selected
using this strategy. See, Anderson, Magliery, Schultz, Exploring
the Limits of Codon and Anticodon Size, Chemistry & Biology,
9:237-244 (2002). These extended codons, some of which are newly
identified, can be useful for the incorporation of multiple
unnatural amino acids in vitro and for in vivo protein
mutagenesis.
Example 7
Generation of an Orthogonal tRNA-Synthetase for
p-aminophenylalanine
[0284] To generate an orthogonal synthetase pair for
p-aminophenylalanine (pAF), the Methanococcus jannaschii
tyrosyl-tRNA synthetase (TyrRS) and mutant tyrosine amber
suppressor tRNA (TyrCUA mutRNA) pair were used as a starting point.
See, Wang, L., Magliery, T. J., Liu, D. R. & Schultz, P. G. A
new functional suppressor tRNA/aminoacyl-tRNA synthetase pair for
the in vivo incorporation of unnatural amino acids into proteins.
J. Am. Chem. Soc. 122:5010-5011 (2000); and, Wang, L. &
Schultz, P. G. Chem. and Biol. 8:883 (2001). The pAF specific
synthetase (pAFRS) was generated by modifying the amino acid
specificity of the Methanococcus jannaschii TyrRS to accept pAF and
not any of the common twenty amino acids. A combination of positive
selections and negative screens was used to identify the pAFRS
enzyme from a library of TyrRS variants 12 containing random amino
acids at five positions (Tyr.sup.32, Glu.sup.107, Asp.sup.158,
Ile.sup.159, and Leu.sup.162). See, Wang, L., Brock, A., Herberich,
B. & Schultz, P. G. Expanding the genetic code of Escherichia
coli. Science 292:498-500 (2001). A single reporter plasmid was
used for both selection and screening. For example, the reporter
plasmid is pREP(2)/YC-JYCUA, which contains the genes for CAT, T7
RNA polymerase, GFP, and TyCUA mutRNA, and a selectable marker for
Tet resistance. The CAT gene contains a TAG codon substitution at
position D112. The T7 RNA polymerase gene contains a seven-amino
acid N-terminal leader peptide and TAG substitutions at M1 and
Q107.
[0285] The positive selection is based on suppression of a TAG
codon at a permissive position within the chloramphenicol
acetyltransferase (CAT) gene by either pAF or an endogenous amino
acid. See, e.g., Wang et al. (2001), supra; and, Pastrnak, M.,
Magliery, T. J. & Schultz, P. G. A new orthogonal suppressor
tRNA/aminoacyl-tRNA synthetase pair for evolving an organism with
an expanded genetic code. Helvetica Chemica Acta 83:2277 (2000).
Cells containing the TyrRS library and reporter plasmid were grown
in liquid culture containing pAF and selected for survival in the
presence of chloramphenicol (Cm). For example, for the positive
selection, cells were grown in GMML minimal media containing 35
.mu.g/ml Kn, 25 .mu.g/ml Tet, 75 .mu.g/ml Cm, and 1 mM pAF
(Sigma).
[0286] The negative screen is based on the inability to suppress in
the absence of pAF two TAG stop codons at permissive positions
within the T7 RNA polymerase gene. Expression of full length T7 RNA
polymerase drives expression of green fluorescent protein (GFP).
Cells from the positive selection were grown in the absence of pAF
and Cm, and then screened using fluorescence activated cell sorting
(FACS) for a lack of fluorescence. For example, for the negative
screen, cells were grown in GMML media containing 35 .mu.g/ml Kn,
25 .mu.g/ml Tet, and 0.002% arabinose. FACS was carried out using a
BDIS FACVantage TSO cell sorter with a Coherent Enterprise II ion
laser. The excitation wavelength was 351 nm and emission was
detected using a 575/25 nm bandpass filter. Collected cells were
diluted into at least 10 volumes of LB, containing Tet and Kn, and
grown to saturation.
[0287] The desired pAFRS was identified following two rounds of
positive selection in liquid media, one round of negative
screening, another round of positive selection in liquid media, and
one round of positive selection on plates. The pAFRS enzyme
contains five mutations relative to the wild type TyrRS(Y32T,
E107T, D158P, 1159L, and L162A). In the absence of pAF, the
IC.sub.50 of cells expressing the selected pAFRS and reporter
plasmid was 10 .mu.g/ml Cm on GMML minimal media plates. The Icso
was 120 .mu.g/ml Cm with 1 mMpAF. Thus, pAF is selectively
suppressing the UAG codon.
Example 8
Evolution of an Aminoacyl-tRNA Synthetase Using
Fluorescence-Activated Cell Sorting
[0288] A FACs based screening system was used to rapidly evolve
three highly selective synthetase variants that accept amino-,
isopropyl-, or allyl-containing tyrosine analogues. The system
included a multipurpose reporter plasmid used for application of
both positive and negative selection pressure and for the facile
and quantitative evaluation of synthetase activity. A
chloramphenicol acetyl transferase (CAT) marker allowed positive
selection for activity of the M. jannaschii tyrosyl-tRNA synthetase
(TyrRS). A T7 polymerase/GFP reporter system allowed assessment of
synthetase activity within cells grown in both the presence and
absence of an unnatural amino acid. Fluorescence activated cell
sorting (FACS) was used to screen against synthetase variants that
accept natural amino acids, while visual and fluorimetric analyses
were to assess synthetase activity qualitatively and
quantitatively, respectively.
[0289] Design of an amplifiable fluorescence reporter system.
Efforts to develop a versatile screening system for the assessment
of synthetase activity in living cells initially arose out of a
desire for a greater degree of control over the selective pressure
applied to populations of synthetase variants, especially negative
selective pressure. As the system was to be used to assess the
activities of large numbers of synthetase variants, a reporter was
sought that would be amenable to high-throughput screening. In
addition, a reporter that would allow for facile qualitative and
quantitative evaluation of synthetase activity was desired. To meet
these requirements, a fluorescence-based screen was designed. The
system was based on the synthetase-dependent production of GFPuv, a
variant of the green fluorescent protein that has been optimized
for expression in E. coli (see, Crameri, A., Whitehorn, E. A.,
Tate, E. & Stemmer, W. P., Nature Biotechnol. 1996, 14,
315-319). This fluorophore is amenable to use in FACS and
fluorimetry, as well as visual inspection on plates and in liquid
culture. The system was designed such that synthetase-dependent
suppression of selector, e.g., amber nonsense codons would result
in the production of a fluorescence signal. In order to maximize
the sensitivity of the reporter, it was made amplifiable by
placement of the amber codons within the gene for T7 RNA
polymerase, which was designed to drive expression of the GFPuv
reporter gene in analogy to other amplifiable intracellular
reporter systems (see, Lorincz, M., Roederer, M., Diwu, Z.,
Herzenberg, L. A., Nolan, G. P. Cytometry, 1996, 24, 321-329; and
Zlokarnik, G., Negulescu, P. A., Knapp, T. E., Mere, L., Burres,
N., Feng, L., Whitney, M., Roemer, K. & Tsien, R. Y., Science,
1998, 279, 84-88). The T7 RNA polymerase gene was placed under
control of the arabinose promoter in order to allow facile
optimization of the production of the RNA transcript for amber
codon-containing T7 RNA polymerase.
[0290] Optimization of the T7 RNA polymerase/GFPuv reporter system.
A medium-copy reporter plasmid, pREP, was designed to express
amber-containing T7 RNA polymerase variants under control of the
arabinose promoter and the GFPuv gene under control of the T7
promoter (FIG. 17a). A series of twelve T7 RNA polymerase variants,
designed to optimize synthetase-dependent fluorescence enhancement
(FIG. 17b), were inserted into pREP to create plasmids pREP(1-12).
All variants contained an N-terminal leader sequence of seven amino
acids (MTMITVH) and 1-3 amber stop codons (TAG). Variants 1-3
contained one, two, and three amber stop codons, respectively,
substituted for the original methionine at position one (M1), just
downstream of the leader sequence. Variants 4-9 contained an amber
codon substituted for D10, R96, Q107, A159, Q169, or Q232,
respectively, which were predicted to be located in loop regions of
the structure (see, Jeruzalmi, D. & Steitz, T. A., EMBO J.,
1998, 17, 41014113). Variants 10-12 contained amber stop codons
substituted at positions M1 and either Q107, A159, or Q232,
respectively. Plasmid constructs were evaluated by fluorimetry and
flow cytometry of live cells for fluorescence enhancement using a
compatible plasmid containing the orthogonal glutaminyl-tRNA
synthetase and Glutamine tRNA.sub.CUA from S. cerevisiae. Plasmids
pREP(1-12) were found to provide varying levels of
synthetase-dependent fluorescence enhancement, with the best
construct, pREP(10) exhibiting 220-fold greater fluorescence by
fluorimetry (FIG. 17c) and .about.400-fold greater median
fluorescence by cytometry (FIG. 17d) in cells containing the wild
type synthetase versus an inactive mutant. Substitution of a
variety of functional groups at positions corresponding to the
amber codons within pREP(10) demonstrate that position 107 within
T7 RNA polymerase is highly permissive.
[0291] Construction of a multipurpose reporter plasmid. In order to
construct a multipurpose plasmid to be used both for selecting and
screening variants of a M. jannaschii TyrRS, plasmid pREP(10) was
combined with plasmid pYC-J17 (see, Wang, L, Brock, A., Herberich,
B. & Schultz, P. G., Science, 2001, 292,498-500) to obtain
pREP/YC-JYCUA (FIG. 25a). Plasmid pREP/YC-JYCUA was assayed for
function with a compatible plasmid expressing a variant of M.
jannaschii TyrRS (pBK-mJYRS; Wang, L, Brock, A., Herberich, B.
& Schultz, P. G., Science, 2001, 292, 498-500) selective for
incorporating O-Methyl-Tyrosine (OMY). Cells containing
pREP/YC-JYCUA and pBK-mJYRS, grown in the presence of OMY,
exhibited a chloramphenicol (Cm) IC.sub.50 value of 120
.mu.g/.mu.l, identical to that obtained using plasmid pYC-J17, and
a fluorescence enhancement of 330-fold for cells grown in the
presence versus the absence of OMY, as measured by fluorimetry.
[0292] Evolution of the substrate specificity of the M. jannaschii
tyrosyl-tRNA synthetase. Results have shown that the amino acid
side chain binding pocket of the M. jannaschii TyrRS can be evolved
to selectively accommodate chemical groups other than the phenol
side chain of tyrosine (see, Wang, L, Brock, A., Herberich, B.
& Schultz, P. G., Science, 2001, 292,498-500; Wang, L., Brock,
A. & Schultz, P. G. J. Am. Chem. Soc. 2002, 124, 1836-1837). We
sought to further explore the generality of unnatural amino acid
accommodation by M. jannaschii TyrRS by challenging the enzyme to
accept four new functionalities: p-Isopropyl-Phenylalanine (pIF),
p-Amino-Phenylalanine (pAF), p-Carboxyl-Phenylalanine (pCF), or
O-Allyl-Tyrosine (OAT) (FIG. 25b). A library of M. jannaschii TyrRS
variants containing randomizations at positions Y32, E107, D158,
1159, and L162 (Wang, L, Brock, A., Herberich, B. & Schultz, P.
G., Science, 2001, 292, 498-500), residues thought to form the
binding pocket for the para position of the tyrosyl ring, was
introduced into cells containing plasmid pREP/YC-JYCUA. These
cells, encompassing a library diversity of .about.10.sup.9, were
used to begin four evolution experiments to identify synthetase
variants selective for pIF, pAF, pCF, or OAT (FIG. 25b). Two cycles
of positive selection were carried out by allowing the cell
cultures to grow to saturation in the presence of Cm and one of the
four unnatural amino acids. Cell aliquots were removed following
the second cycle of positive selection and used to inoculate a new
culture containing no added amino acid or Cm, and the culture was
again allowed to grow to saturation. At this point, cells that
fluoresce are likely to contain synthetase variants that can accept
one of the 20 natural amino acids. Approximately 10.sup.8 cells
from each line were subjected to negative screening using FACS in
order to eliminate natural amino acid-accepting synthetase
variants. The non-fluorescent cells were collected and amplified
through growth to saturation. These amplified cells were used to
inoculate a new culture for a final cycle of positive selection in
liquid culture containing unnatural amino acid and Cm. Following
growth to saturation, each population of cells was plated on media
containing 0, 30, 60, or 100 .mu.g/mL Cm and either 0 or 1 mM of
the appropriate unnatural amino acid.
[0293] Identification and characterization of evolved synthetase
variants. Cm plates supplemented with pIF, pAF, and OAT produced
10-100-fold greater numbers of fluorescent colonies than plates
containing no added amino acid. In contrast, plates for the pCF
population produced the same number of fluorescent colonies with or
without addition of pCF. The ten largest fluorescent colonies were
picked for each of the pIF, pAF, and OAT populations from unnatural
amino acid-containing plates and grown to saturation in liquid
media with or without added unnatural amino acid. A qualitative
assessment of fluorescence production was made visually with the
use of a hand-held long-wavelength ultraviolet lamp (FIG. 23a).
[0294] Synthetase variants corresponding to clones producing
significant differences in fluorescence were sequenced. All ten
clones from the pIF and pAF populations had identical sequences,
while three different clones were identified from the OAT
population. Amino acid changes occurred within the five randomized
sites in all clones, with the exception of two additional
substitutions within the pIF-tRNA synthetase (pIF-RS) variant. The
activities of the different clones were quantitatively assessed.
Fluorescence was measured fluorimetrically for cells grown in
liquid culture in the presence or absence of unnatural amino acid
(FIG. 23b). The Cm IC.sub.50s were determined by plating the cells
on varying concentrations of Cm in the presence or absence of
unnatural amino acid (FIG. 23c).
[0295] A myoglobin gene containing an amber codon in the fourth
position was used to assess the production of unnatural amino
acid-containing protein. The gene was expressed in cells, using the
pIF-RS, pAF-RS, or OMY-RS variant, respectively, in either the
presence or absence of pIF, pAF, or OAT (FIG. 23d). Protein yields
were comparable for all three variants, ranging from 1-2 milligrams
of protein per liter of unnatural amino acid-containing cell
culture. In contrast, protein production was virtually undetectable
in cultures grown in the absence of unnatural amino acid. Proteins
were analyzed by electrospray mass spectrometry, giving masses of
18457.40.+-.0.81 (18457.28 expected) for the pIF-containing
protein, and 18430.30.+-.0.27 (18430.21 expected) for the
pAF-containing protein. Activity measurements obtained using the Cm
IC.sub.50, fluorimetry, and protein expression analyses correlated
well, however the activity of the pIF-RS appears to be somewhat
underestimated by fluorimetry. As compared to other assays, the
disproportionately low fluorimetry measurement for the pIF-RS
variant, suggests that T7 RNA polymerase may be partially
destabilized upon incorporation of the pIF analogue, despite the
apparent permissivity of the amber positions within the reporter
(see, FIG. 17c).
[0296] Utility of the multipurpose reporter system. The reporter
system described here allows the use of a single multipurpose
plasmid for both positive selection and negative screening,
obviating the need to shuttle plasmids between alternating rounds
of positive and negative selection. A total of only three rounds of
positive selection and one round of negative screening were
required to enable the identification of synthetase variants that
selectively accept desired unnatural amino acids. These features
allow evolution experiments to be carried out in a matter of days.
The screening system can be used to readily identify active
synthetase variants using agar plates containing unnatural amino
acid and to individually assay the amino acid specificity of the
variants.
[0297] As described above, the T7 RNA polymerase/GFP system can be
used to quantitatively compare the activities of synthetase
variants. The availability of the three OAT-RS clones described
here and a different OAT-RS clone derived independently from the
same library using a positive/negative selection based on CAT and
barnase allows the possibility of comparing the two different
evolution systems in terms of the synthetase variants resulting
from each. This analysis reveals that the three clones derived from
positive selection and negative screening exhibit slightly lower
levels of fluorescence in the presence of OAT, but .about.10-fold
lower background levels in the absence of the unnatural amino acid.
The fluorescence enhancement for cells grown in the presence versus
the absence of the unnatural amino acid is thus about 6-fold higher
for cells expressing OAT-RS(1) from selection and screening than
for cells expressing the OAT-RS clone derived from
positive/negative selection using barnase. Although it is not clear
whether this example is representative, these data suggest that the
T7 RNA polymerase/GFP system may allow more stringency in selecting
against synthetase variants that are promiscuous towards natural
amino acid substrates. However, the fluorescence enhancement for
cells grown in the presence versus the absence of an unnatural
amino acid is expected to represent a lower limit for the fidelity
of unnatural amino acid incorporation, as competition of unnatural
amino acids for being bound by an evolved synthetase variant would
reduce binding of natural amino acids. Moreover, although high
fidelity is clearly desirable, there is likely to be a trade-off
between fidelity and overall synthetase activity, which may depend
on the desired application.
[0298] Generality of aminoacyl tRNA synthetase evolution. Previous
results and those presented here demonstrate that the amino acid
side chain binding pocket of the M. jannaschii TyrRS is quite
malleable. The enzyme can be evolved to accommodate a variety of
functionalities in place of the phenol side chain of tyrosine and
can do so with high selectivity. In this application it was
demonstrated that enzyme can be evolved to accommodate an amine,
isopropyl, or allyl ether functionality at the para position of the
tyrosine ring, instead of hydroxyl. It was not possible to identify
an enzyme variant that could accept the pCF unnatural amino acid. A
second attempt to evolve a synthetase to accept the pCF amino acid
was also unsuccessful. Using LC/MS analysis, pCF could not be
detected upon toluenization of E. coli cells grown in the presence
of the unnatural amino acid, suggesting that pCF is not transported
into cells or that it is metabolized upon entry.
[0299] Of the three successful evolution experiments described
here, only the evolution of the OAT-RS resulted in the
identification of more than one active clone. The OAT-RS evolution
was also the experiment that produced the most active synthetase
variant. These results suggest that some amino acid specificities
may be easier to select for than others. This could be due, in
part, to the relative difficulty of selectively recognizing
different unnatural amino acids in the context of the 20 natural
amino acids. It may be, for example, that pAF, due to its
structural and electronic similarities to tyrosine, is more
difficult to selectively recognize than OAT. This would explain why
a greater number of OAT-RS clones were identified than pAF-RS
clones and why the pAF-RS clone is less active than the best OAT-RS
clone.
[0300] Plasmid Construction. Plasmid pREP (FIG. 17a) was
constructed by insertion of a BamHI/ApaLI overlap PCR fragment
containing the T7 RNA polymerase gene upstream of an mmB
transcription termination region, followed by an ApaLI/AhdI overlap
PCR fragment containing the araC gene and ara promoter region from
the pBAD/Myc-His A plasmid (Invitrogen; for transcriptional control
of the T7 RNA polymerase gene) and the GFPuv gene (Clontech;
upstream of the T7 terminator region and downstream of the T7
promoter) between the AhdI/BamHI sites of plasmid pACYC177 (New
England Biolabs). Plasmids pREP(1-12) were constructed by
replacement of an HpaI/ApaLI fragment of T7 RNA polymerase with
overlap PCR fragments containing amber mutations at the positions
described. Plasmid pREP/YC-JYCUA was constructed by ligation of an
AfeI/SacII fragment from pREP(10) and an EarI(blunted)/SacII
fragment from pYC-J17 (Wang, L, Brock, A., Herberich, B. &
Schultz, P. G., Science, 2001, 292, 498-500). The desired construct
was identified following transformation into cells containing
plasmid pQ screening for fluorescence.
[0301] Plasmid pQ was constructed by triple ligation of a
AatII/SalI overlap PCR fragment containing the SCQRS downstream of
the lac promoter region and upstream of the E. coli QRS termination
region, a SalI/AvaI overlap PCR fragment containing the S.
cerevisiae tRNA(CUA).sup.Gln downstream of the Ipp promoter region
and upstream of an rrnC termination region, and the AvaI/AatII
fragment of pBR322 (New England Biolabs). Plasmid pQD was
constructed by replacement of pQ fragment between BamHI and BglII
with a BamHI/BglII fragment of the SCQRS(D291A) mutant.
[0302] Plasmid pBAD/JYAMB-4TAG was constructed by insertion of a
PCR fragment of the S4Amber mutant of myoglobin, containing a
C-terminal 6His-tag, into the pBAD/YC-JYCUA plasmid, a hybrid of
plasmid pYC-J17 (Wang, L, Brock, A., Herberich, B. & Schultz,
P. G., Science, 2001, 292, 498-500) and pBAD/Myc-His A (Invitrogen)
containing the gene for MjYtRNAcUA, and the pBAD promoter and
cloning regions for heterologous expression of an inserted
gene.
[0303] Fluorimetric and cytometric analyses. Single colonies
containing desired plasmids were used to inoculate 2-mL GMML
cultures containing the appropriate antibiotics, 0.002% Arabinose,
and an appropriate unnatural amino acid, if desired. Cultures were
grown to saturation and cells (200 .mu.L) were pelleted and
resuspended in 1 mL phosphate-buffered saline (PBS). Cell
concentrations were analyzed by absorbance at 600 nm and
fluorescence levels were measured at 505 nm with excitation at 396
nm using a FluoroMax-2 fluorimeter. Cells suspended in PBS were
analyzed cytometrically. To evaluate the permissivity of the amber
positions within the T7 polymerase gene of pREP(10), the reporter
plasmid was transformed into a panel of suppressor strains, which
were subsequently analyzed fluorimetrically.
[0304] Evolution of aminoacyl-tRNA synthetase variants. M.
jannaschii TyrRS variants randomized at positions Y32, E107, D158,
1159, and L162 (Wang, L, Brock, A., Herberich, B. & Schultz, P.
G., Science, 2001, 292, 498-500) were transformed into DH10B E.
coli cells (Life Technologies) containing pREP/YC-JYCUA to generate
a library with a diversity of .about.10.sup.9. Transformants were
allowed to recover in SOC medium for 60 min at 37.degree. C., and
were grown to saturation in LB medium. To begin an initial positive
selection, 2 mL of library culture, pelleted and resuspended in GM
medium, was used to inoculate 500 mL of GMML containing 25 .mu.g/mL
Tetracycline (Tet), 35 .mu.g/mL Kanamycin (Kn), and 1 mMpIF, pAF,
pCF, or OAY. After incubation for 3 hours at 37.degree. C., Cm was
added to a final concentration of 75 .mu.g/mL and cells were grown
to saturation (.about.48 hours). For the second positive selection,
a 100-mL GMML culture containing Tet, Kn, 75 .mu.g/mL Cm, and 1
mMpIF, pAF, pCF, or OAY was inoculated with cells from the initial
positive selection (500 .mu.L) and grown to saturation at
37.degree. C. (.about.24-36 hours). In preparation for negative
screening, a 25-mL GMML culture containing Tet, Kn, and 0.02%
arabinose (Ara) was inoculated with cells from the second positive
selection (100 .mu.L, pelleted and resuspended in GMML) and grown
to saturation at 37.degree. C. (.about.24 hours). Ara-induced cells
grown in the absence of unnatural amino acids (1 mL) were pelleted
and resuspended in 3 mL of phosphate-buffered saline (PBS). Cells
were sorted for lack of expression of GFPuv using a BDIS FACVantage
TSO cell sorter with a Coherent Enterprise II ion laser with
excitation at 351 nm and emissions detected using a 575/25 nm
bandpass filter. Collected cells were diluted in at least 10
volumes of LB, containing Tet and Kn, and grown to saturation. To
begin the third round of positive selection, 100 .mu.L of cells
from the negative screen were pelleted, resuspended in GMML, and
used to inoculate 25 mL of GMML containing Tet, Kn, and 1 mM pIF,
pAF, pCF, or OAY. After incubation for 3 hours at 37.degree. C., Cm
was added to a final concentration of 75 .mu.g/mL and cells were
grown to saturation (.about.24 hours). Following the third positive
selection, cells were plated on GMM agar containing Tet, Kn, 0.002%
Ara, 0, 75, or 100 .mu.g/mL Cm, and 0 or 1 mMpIF, pAF, pCF, or OAY,
and grown for 48 hours at 37.degree. C.
[0305] Expression and characterization of unnatural amino
acid-containing proteins. DH10B cells co-transformed with
pBAD/JYAMB4TAG and the appropriate pBK plasmid were used to
inoculate a 100-mL GMML starter culture containing Kn and Tet,
which was grown to saturation. A 500-mL culture containing Kn, Tet,
0.002% Ara, 5 .mu.M FeCl.sub.3, and the desired unnatural amino
acid (or none) was inoculated with 50 mL of the starter culture and
grown to saturation (.about.18 hours). Cultures were pelleted,
sonicated, and the myoglobin protein isolated according to the
protocol of the QiaExpressionist (Qiagen) His-tag purification kit.
Proteins were analyzed electrophoretically on a 12-20% gradient SDS
polyacrylamide gel and by electrospray mass spectrometry.
Example 9
Orthogonal tRNA/Threonyl-tRNA Synthetase Pair
[0306] This example illustrates the generation of an orthogonal
tRNA/Threonyl-tRNA synthetase pair. FIG. 27 illustrates a
threonyl-tRNA synthetase from Thermus thermophilus. This synthetase
has two N-terminal editing domains, a catalytic domain and a
C-terminal anticodon binding domain (659 amino acids). To generate
the orthogonal synthetase based on the T. thernophilus synthetase,
the editing domain(s), N1 or N1 and N2 was deleted from the
synthetase to generate an N-truncated T. thermophilus ThrRS (475
amino acids). This synthetase has the same catalytic activity but
lacks the proofreading activity. The N-truncated synthetase was
screened for activity. The N-truncated synthetase did not
aminoacylate Escherichia coli tRNA.
[0307] Because, the T. thermophilus tRNAThr was found to be a
substrate for Escherichia coli Threonyl-tRNA synthetase, the T.
thermophilus tRNAThr was mutated in order to generate an orthogonal
pair. FIG. 28 illustrates the mutations made in the tRNA.
Specifically, C2G71 was mutated to A2U71. In vitro charging
experiments demonstrate that this mutant is not a substrate for the
E. coli Threonyl-tRNA synthetase but is a good substrate for the T.
thermophilus Threonyl-tRNA synthetase. Another mutant was also
constructed, which included the following
mutations:--C2G71.fwdarw.A2U71 and G34G35U36.fwdarw.C34G35U36 in
order to generate an amber suppressor tRNA. Other mutant tRNAs with
modified anticodon loops in addition to C2G71.fwdarw.A2U71 were
also generated to suppress three and four base codons such as TGA,
ACCA, ACAA, AGGA, CCCT, TAGA, and CTAG. All these tRNAs were not as
good as substrate as the wild type tRNAThr (with A2U71) but can be
improved by mutating the anticodon binding site of the T.
thermophilus Threonyl-tRNA synthetase.
Example 10
Sequences of Exemplary O-tRNAs and O-RSs
[0308] Exemplary O-tRNAs comprise a nucleic acid comprising a
polynucleotide sequence selected from the group consisting of: SEQ
ID NO:1-3 and/or a complementary polynucleotide sequence thereof.
See, Table 5, Appendix 1. Similarly, example O-RS include
polypeptides selected from the group consisting of: a polypeptide
comprising an amino acid sequence selected from the group
consisting of SEQ ID NO: 35-66 and a polypeptide encoded by a
nucleic acid comprising a polynucleotide sequence selected from the
group consisting of: SEQ ID NO:4-34 and a complementary
polynucleotide sequence thereof.
[0309] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
All publications, patents, and patent applications cited herein are
hereby incorporated by reference in their entirety for all
purposes.
Sequence CWU 1
1
108 1 77 DNA Methanococcus jannaschii 1 ccggcggtag ttcagcaggg
cagaacggcg gactctaaat ccgcatggcg ctggttcaaa 60 tccggcccgc cggacca
77 2 88 DNA Halobacterium sp. NRC-1 2 cccagggtag ccaagctcgg
ccaacggcga cggactctaa atccgttctc gtaggagttc 60 gagggttcga
atcccttccc tgggacca 88 3 89 DNA Halobacterium sp. NRC-1 3
gcgagggtag ccaagctcgg ccaacggcga cggacttcct aatccgttct cgtaggagtt
60 cgagggttcg aatccctccc ctcgcacca 89 4 921 DNA Methanococcus
jannaschii 4 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gctcagatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttggc
tgatttacac gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtac tttccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa tgcaattcat 480 tatcctggcg ttgatgttgc agttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggga
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt tagtagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 5
917 DNA Methanococcus jannaschii 5 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctgggatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatgtgctt atggaagtcc tttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat ggttatcatt 480 atcttggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 6 917 DNA Methanococcus jannaschii 6
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctcagatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtcc tttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
tgttctcatt 480 attatggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 7 917 DNA
Methanococcus jannaschii 7 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctactatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtac gttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat ccgttgcatt 480 atgctggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 8 917 DNA Methanococcus jannaschii 8
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctcatatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtga gttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
cggccgcatt 480 atcctggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 9 917 DNA
Methanococcus jannaschii 9 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gcttatatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtcc tttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat cagagtcatt 480 atgatggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 10 917 DNA Methanococcus jannaschii 10
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gcttcgatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtac gttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
acgtatcatt 480 atgctggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 11 917 DNA
Methanococcus jannaschii 11 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctcctatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtat gttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat aatacgcatt 480 atgggggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 12 917 DNA Methanococcus jannaschii 12
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctacgatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtca tttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
cagactcatt 480 atgagggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 13 917 DNA
Methanococcus jannaschii 13 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctcatatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtaa gttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat ccgtgtcatt 480 atcatggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 14 917 DNA Methanococcus jannaschii 14
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctgctatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtcg gttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
gtgattcatt 480 atgatggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 15 917 DNA
Methanococcus jannaschii 15 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctgggatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtac tttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat acgtattatt 480 atgctggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 16 917 DNA Methanococcus jannaschii 16
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctctgatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtcc gttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
cagattcatt 480 ctagtggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 17 921 DNA
Methanococcus jannaschii 17 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctgacatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtga attccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agcaagagag 420 gatgaaaatc caaaggttgc
tgaagttatc tatccaataa tgcaggttaa tggaatgcat 480 tatcaaggcg
ttgatgttgc agttggaggg atggagcaga gaaaaataca catgttagca 540
agggagcttt taccaaaaaa ggttgtttgt attcacaacc ctgtcttaac gggtttggat
600 ggagaaggaa agatgagttc ttcaaaaggg aattttatag ctgttgatga
ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac tgcccagctg
gagttgttga aggaaatcca 720 ataatggaga tagctaaata cttccttgaa
tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag atttgacagt
taatagctat gaggagttag agagtttatt taaaaataag 840 gaattgcatc
caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag 900
ccaattagaa agagattata a 921 18 921 DNA Methanococcus jannaschii 18
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gcttacatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtct attccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agcaagagag
420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa tgcaggttaa
tgatattcat 480 tatacaggcg ttgatgttgc agttggaggg atggagcaga
gaaaaataca catgttagca 540 agggagcttt taccaaaaaa ggttgtttgt
attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa agatgagttc
ttcaaaaggg aattttatag
ctgttgatga ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac
tgcccagctg gagttgttga aggaaatcca 720 ataatggaga tagctaaata
cttccttgaa tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag
atttgacagt taatagctat gaggagttag agagtttatt taaaaataag 840
gaattgcatc caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag
900 ccaattagaa agagattata a 921 19 921 DNA Methanococcus jannaschii
19 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gctctaatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttgac
agatttaaac gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtga attccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa tgatattcat 480 tatttaggcg ttgatgttgc agttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt taatagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 20
921 DNA Methanococcus jannaschii 20 atggacgaat ttgaaatgat
aaagagaaac acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt
taaaaaaaga tgaaaaatct gctctaatag gttttgaacc aagtggtaaa 120
atacatttag ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt
180 gatataatta tattgttgac agatttaaaa gcctatttaa accagaaagg
agagttggat 240 gagattagaa aaataggaga ttataacaaa aaagtttttg
aagcaatggg gttaaaggca 300 aaatatgttt atggaagtga attccagctt
gataaggatt atacactgaa tgtctataga 360 ttggctttaa aaactacctt
aaaaagagca agaaggagta tggaacttat agcaagagag 420 gatgaaaatc
caaaggttgc tgaagttatc tatccaataa tgtcagttaa tgtaattcat 480
tatttaggcg ttgatgttgt agttggaggg atggagcaga gaaaaataca catgttagca
540 agggagcttt taccaaaaaa ggttgtttgt attcacaacc ctgtcttaac
gggtttggat 600 ggagaaggaa agatgagttc ttcaaaaggg aattttatag
ctgttgatga ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac
tgcccagctg gagttgttga aggaaatcca 720 ataatggaga tagctaaata
cttccttgaa tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag
atttgacagt taatagctat gaggagttag agagtttatt taaaaataag 840
gaattgcatc caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag
900 ccaattagaa agagattata a 921 21 921 DNA Methanococcus jannaschii
21 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gctctaatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttgcc
agatttatca gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtga attccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa tgatattcat 480 tatttaggcg ttgatgttgc agttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt taatagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 22
921 DNA Methanococcus jannaschii 22 atggacgaat ttgaaatgat
aaagagaaac acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt
taaaaaaaga tgaaaaatct gctacaatag gttttgaacc aagtggtaaa 120
atacatttag ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt
180 gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg
agagttggat 240 gagattagaa aaataggaga ttataacaaa aaagtttttg
aagcaatggg gttaaaggca 300 aaatatgttt atggaagtga attccagctt
gataaggatt atacactgaa tgtctataga 360 ttggctttaa aaactacctt
aaaaagagca agaaggagta tggaacttat agcaagagag 420 gatgaaaatc
caaaggttgc tgaagttatc tatccaataa tgcaggttaa tgatattcat 480
tatgcaggcg ttgatgttgc agttggaggg atggagcaga gaaaaataca catgttagca
540 agggagcttt taccaaaaaa ggttgtttgt attcacaacc ctgtcttaac
gggtttggat 600 ggagaaggaa agatgagttc ttcaaaaggg aattttatag
ctgttgatga ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac
tgcccagctg gagttgttga aggaaatcca 720 ataatggaga tagctaaata
cttccttgaa tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag
atttgacagt taatagctat gaggagttag agagtttatt taaaaataag 840
gaattgcatc caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag
900 ccaattagaa agagattata a 921 23 921 DNA Methanococcus jannaschii
23 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gctacaatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttgtc
cgatttacca gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtga attccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa tgatattcat 480 tatttaggcg ttgatgttgc agttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt taatagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 24
921 DNA Methanococcus jannaschii 24 atggacgaat ttgaaatgat
aaagagaaac acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt
taaaaaaaga tgaaaaatct gctacaatag gttttgaacc aagtggtaaa 120
atacatttag ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt
180 gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg
agagttggat 240 gagattagaa aaataggaga ttataacaaa aaagtttttg
aagcaatggg gttaaaggca 300 aaatatgttt atggaagtat gttccagctt
gataaggatt atacactgaa tgtctataga 360 ttggctttaa aaactacctt
aaaaagagca agaaggagta tggaacttat agcaagagag 420 gatgaaaatc
caaaggttgc tgaagttatc tatccaataa tgcaggttaa ttcatcacat 480
tatgacggcg ttgatgttgc agttggaggg atggagcaga gaaaaataca catgttagca
540 agggagcttt taccaaaaaa ggttgtttgt attcacaacc ctgtcttaac
gggtttggat 600 ggagaaggaa agatgagttc ttcaaaaggg aattttatag
ctgttgatga ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac
tgcccagctg gagttgttga aggaaatcca 720 ataatggaga tagctaaata
cttccttgaa tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag
atttgacagt taatagctat gaggagttag agagtttatt taaaaataag 840
gaattgcatc caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag
900 ccaattagaa agagattata a 921 25 921 DNA Methanococcus jannaschii
25 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gctcaaatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttgcc
agatttacac gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtga attccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa tgatattcat 480 tatttaggcg ttgatgttga cgttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt taatagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 26
921 DNA Methanococcus jannaschii 26 atggacgaat ttgaaatgat
aaagagaaac acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt
taaaaaaaga tgaaaaatct gctcacatag gttttgaacc aagtggtaaa 120
atacatttag ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt
180 gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg
agagttggat 240 gagattagaa aaataggaga ttataacaaa aaagtttttg
aagcaatggg gttaaaggca 300 aaatatgttt atggaagtgc attccagctt
gataaggatt atacactgaa tgtctataga 360 ttggctttaa aaactacctt
aaaaagagca agaaggagta tggaacttat agcaagagag 420 gatgaaaatc
caaaggttgc tgaagttatc tatccaataa tgcaggttaa tggacaccat 480
tatataggcg ttgatgttgc agttggaggg atggagcaga gaaaaataca catgttagca
540 agggagcttt taccaaaaaa ggttgtttgt attcacaacc ctgtcttaac
gggtttggat 600 ggagaaggaa agatgagttc ttcaaaaggg aattttatag
ctgttgatga ctctccagaa 660 gagattaggg ctaagataaa gaaagcatac
tgcccagctg gagttgttga aggaaatcca 720 ataatggaga tagctaaata
cttccttgaa tatcctttaa ccataaaaag gccagaaaaa 780 tttggtggag
atttgacagt taatagctat gaggagttag agagtttatt taaaaataag 840
gaattgcatc caatggattt aaaaaatgct gtagctgaag aacttataaa gattttagag
900 ccaattagaa agagattata a 921 27 921 DNA Methanococcus jannaschii
27 atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga
ggaagagtta 60 agagaggttt taaaaaaaga tgaaaaatct gcttacatag
gttttgaacc aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa
aagatgattg atttacaaaa tgctggattt 180 gatataatta tattgttggc
tgatttacac gcctatttaa accagaaagg agagttggat 240 gagattagaa
aaataggaga ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300
aaatatgttt atggaagtgc attccagctt gataaggatt atacactgaa tgtctataga
360 ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat
agcaagagag 420 gatgaaaatc caaaggttgc tgaagttatc tatccaataa
tgcaggttaa ttgcgcacat 480 tatttaggcg ttgatgttgc agttggaggg
atggagcaga gaaaaataca catgttagca 540 agggagcttt taccaaaaaa
ggttgtttgt attcacaacc ctgtcttaac gggtttggat 600 ggagaaggaa
agatgagttc ttcaaaaggg aattttatag ctgttgatga ctctccagaa 660
gagattaggg ctaagataaa gaaagcatac tgcccagctg gagttgttga aggaaatcca
720 ataatggaga tagctaaata cttccttgaa tatcctttaa ccataaaaag
gccagaaaaa 780 tttggtggag atttgacagt taatagctat gaggagttag
agagtttatt taaaaataag 840 gaattgcatc caatggattt aaaaaatgct
gtagctgaag aacttataaa gattttagag 900 ccaattagaa agagattata a 921 28
917 DNA Methanococcus jannaschii 28 atggacgaat ttgaaatgat
aaagagaaac acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt
taaaaaaaga tgaaaaatct gctggtatag gttttgaacc aagtggtaaa 120
atacatttag ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt
180 gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg
agagttggat 240 gagattagaa aaataggaga ttataacaaa aaagtttttg
aagcaatggg gttaaaggca 300 aaatatgttt atggaagttc cttccagctt
gataaggatt atacactgaa tgtctataga 360 ttggctttaa aaactacctt
aaaaagagca agaaggagta tggaacttat agaagagagg 420 atgaaaatcc
aaaggttgct gaagttatct atccaataat gcaggttaat acgagtcatt 480
atctgggcgt tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa
540 gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg
ggtttggatg 600 gagaaggaaa gatgagttct tcaaaaggga attttatagc
tgttgatgac tctccagaag 660 agattagggc taagataaag aaagcatact
gcccagctgg agttgttgaa ggaaatccaa 720 taatggagat agctaaatac
ttccttgaat atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga
tttgacagtt aatagctatg aggagttaga gagtttattt aaaaataagg 840
aattgcatcc aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc
900 caattagaaa gagatta 917 29 917 DNA Methanococcus jannaschii 29
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctacgatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtaa tttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
ccgcttcatt 480 atcagggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 30 917 DNA
Methanococcus jannaschii 30 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctacgatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagtct gttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat cctcttcatt 480 atgagggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 31 917 DNA Methanococcus jannaschii 31
atggacgaat ttgaaatgat aaagagaaac acatctgaaa ttatcagcga ggaagagtta
60 agagaggttt taaaaaaaga tgaaaaatct gctcttatag gttttgaacc
aagtggtaaa 120 atacatttag ggcattatct ccaaataaaa aagatgattg
atttacaaaa tgctggattt 180 gatataatta tattgttggc tgatttacac
gcctatttaa accagaaagg agagttggat 240 gagattagaa aaataggaga
ttataacaaa aaagtttttg aagcaatggg gttaaaggca 300 aaatatgttt
atggaagtac tttccagctt gataaggatt atacactgaa tgtctataga 360
ttggctttaa aaactacctt aaaaagagca agaaggagta tggaacttat agaagagagg
420 atgaaaatcc aaaggttgct gaagttatct atccaataat gcaggttaat
ccggttcatt 480 atcagggcgt tgatgttgca gttggaggga tggagcagag
aaaaatacac atgttagcaa 540 gggagctttt accaaaaaag gttgtttgta
ttcacaaccc tgtcttaacg ggtttggatg 600 gagaaggaaa gatgagttct
tcaaaaggga attttatagc tgttgatgac tctccagaag 660 agattagggc
taagataaag aaagcatact gcccagctgg agttgttgaa ggaaatccaa 720
taatggagat agctaaatac ttccttgaat atcctttaac cataaaaagg ccagaaaaat
780 ttggtggaga tttgacagtt aatagctatg aggagttaga gagtttattt
aaaaataagg 840 aattgcatcc aatggattta aaaaatgctg tagctgaaga
acttataaag attttagagc 900 caattagaaa gagatta 917 32 917 DNA
Methanococcus jannaschii 32 atggacgaat ttgaaatgat aaagagaaac
acatctgaaa ttatcagcga ggaagagtta 60 agagaggttt taaaaaaaga
tgaaaaatct gctactatag gttttgaacc aagtggtaaa 120 atacatttag
ggcattatct ccaaataaaa aagatgattg atttacaaaa tgctggattt 180
gatataatta tattgttggc tgatttacac gcctatttaa accagaaagg agagttggat
240 gagattagaa aaataggaga ttataacaaa aaagtttttg aagcaatggg
gttaaaggca 300 aaatatgttt atggaagttc gttccagctt gataaggatt
atacactgaa tgtctataga 360 ttggctttaa aaactacctt aaaaagagca
agaaggagta tggaacttat agaagagagg 420 atgaaaatcc aaaggttgct
gaagttatct atccaataat gcaggttaat ccactgcatt 480 atcagggcgt
tgatgttgca gttggaggga tggagcagag aaaaatacac atgttagcaa 540
gggagctttt accaaaaaag gttgtttgta ttcacaaccc tgtcttaacg ggtttggatg
600 gagaaggaaa gatgagttct tcaaaaggga attttatagc tgttgatgac
tctccagaag 660 agattagggc taagataaag aaagcatact gcccagctgg
agttgttgaa ggaaatccaa 720 taatggagat agctaaatac ttccttgaat
atcctttaac cataaaaagg ccagaaaaat 780 ttggtggaga tttgacagtt
aatagctatg aggagttaga gagtttattt aaaaataagg 840 aattgcatcc
aatggattta aaaaatgctg tagctgaaga acttataaag attttagagc 900
caattagaaa gagatta 917 33 2799 DNA Archaeoglobus fulgidus 33
atgagcgatt tcaggataat tgaggagaag tggcagaagg cgtgggagaa ggacagaatt
60 tttgagtccg atcctaatga gaaggagaag ttttttctca caattcccta
tccttacctt 120 aatggaaatc ttcacgcagg tcacacgaga accttcacaa
ttggcgatgc cttcgccaga 180 tacatgagaa tgaagggcta caacgttctc
tttcccctcg gctttcatgt tacgggcacc 240 ccaatcattg gccttgcgga
gctcatagcc aagagggacg agaggacgat agaggtttac 300 accaaatacc
atgacgttcc gctggaggac ttgcttcagc tcacaactcc agagaaaatc 360
gttgagtact tctcaaggga ggcgctgcag gctttgaaga gcataggcta ctccattgac
420 tggaggaggg ttttcaccac aaccgatgaa gagtatcaga gattcatcga
gtggcagtac 480 tggaagctca aggagcttgg cctgattgtg aagggcaccc
accccgtcag atactgcccc 540 cacgaccaga atcctgttga agaccacgac
cttctcgctg gggaggaggc aactattgtt 600 gaatttaccg ttataaagtt
caggcttgaa gatggagacc tcattttccc ctgtgcaact 660 ctccgtcccg
aaaccgtgtt tggcgtcacg aacatctggg taaagccgac aacctacgta 720
attgccgagg tggatgggga aaagtggttt gtgagcaaag
aggcttacga gaagctcacc 780 tacacggaga aaaaagtcag gctgctggag
gaggttgatg cgtcgcagtt cttcggcaag 840 tacgtcatag tcccgctggt
aaacagaaaa gtgccaattc tgcctgcaga gtttgttgac 900 accgacaacg
caacaggagt tgtgatgagc gttcccgcac acgctccttt tgacctggct 960
gccattgagg acttgaagag agacgaggaa acgctggcga agtacggaat tgacaaaagc
1020 gttgtagaga gcataaagcc aatagttctg attaagacgg acattgaagg
tgttcctgct 1080 gagaagctaa taagagagct tggagtgaag agccagaagg
acaaggagct gctggataag 1140 gcaaccaaga ccctctacaa gaaggagtac
cacacgggaa tcatgctgga caacacgatg 1200 aactatgctg gaatgaaagt
ttctgaggcg aaggagagag ttcatgagga tttggttaag 1260 cttggcttgg
gggatgtttt ctacgagttc agcgagaagc ccgtaatctg caggtgcgga 1320
acgaagtgcg ttgttaaggt tgttagggac cagtggttcc tgaactactc caacagagag
1380 tggaaggaga aggttctgaa tcaccttgaa aagatgcgaa tcatccccga
ctactacaag 1440 gaggagttca ggaacaagat tgagtggctc agggacaagg
cttgtgccag aaggaagggg 1500 cttggaacga gaattccgtg ggataaggag
tggctcatcg agagcctttc agactcaaca 1560 atctacatgg cctactacat
ccttgccaag tacatcaacg caggattgct caaggccgag 1620 aacatgactc
ccgagttcct cgactacgtg ctgctgggca aaggtgaggt tgggaaagtt 1680
gcggaagctt caaaactcag cgtggagtta atccagcaga tcagggacga cttcgagtac
1740 tggtatcccg ttgacctaag aagcagtggc aaggacttgg ttgcaaacca
cctgctcttc 1800 tacctcttcc accacgtcgc cattttcccg ccagataagt
ggccgagggc aattgccgta 1860 aacggatacg tcagccttga gggcaagaag
atgagcaaga gcaaagggcc cttgctaacg 1920 atgaagaggg cggtgcagca
gtatggtgcg gatgtgacga ggctctacat cctccacgct 1980 gcagagtacg
acagcgatgc ggactggaag agcagagagg ttgaagggct tgcaaaccac 2040
ctcaggaggt tctacaacct cgtgaaggag aactacctga aagaggtggg agagctaaca
2100 accctcgacc gctggcttgt gagcaggatg cagagggcaa taaaggaagt
gagggaggct 2160 atggacaacc tgcagacgag gagggccgtg aatgccgcct
tcttcgagct catgaacgac 2220 gtgagatggt atctgaggag aggaggtgag
aacctcgcta taatactgga cgactggatc 2280 aagctcctcg ccccctttgc
tccgcacatt tgcgaggagc tgtggcactt gaagcatgac 2340 agctacgtca
gcctcgaaag ctacccagaa tacgacgaaa ccagggttga cgaggaggcg 2400
gagagaattg aggaatacct ccgaaacctt gttgaggaca ttcaggaaat caagaagttt
2460 gttagcgatg cgaaggaggt ttacattgct cccgccgaag actggaaggt
taaggcagca 2520 aaggtcgttg ctgaaagcgg ggatgttggg gaggcgatga
agcagcttat gcaggacgag 2580 gagcttagga agctcggcaa agaagtgtca
aatttcgtca agaagatttt caaagacaga 2640 aagaagctga tgctagttaa
ggagtgggaa gttctgcagc agaacctgaa atttattgag 2700 aatgagaccg
gactgaaggt tattcttgat actcagagag ttcctgagga gaagaggagg 2760
caggcagttc cgggcaagcc cgcgatttat gttgcttaa 2799 34 2814 DNA
Methanobacterium thermoautotrophicum 34 gtggatattg aaagaaaatg
gcgtgataga tggagagatg ctggcatatt tcaggctgac 60 cctgatgaca
gagaaaagat attcctcaca gtcgcttacc cctaccccag tggtgcgatg 120
cacataggac acgggaggac ctacactgtc cctgatgtct atgcacggtt caagaggatg
180 cagggctaca acgtcctgtt tcccatggcc tggcatgtca caggggcccc
tgtcataggg 240 atagcgcgga ggattcagag gaaggatccc tggaccctca
aaatctacag ggaggtccac 300 agggtccccg aggatgagct tgaacgtttc
agtgaccctg agtacatagt tgaatacttc 360 agcagggaat accggtctgt
tatggaggat atgggctact ccatcgactg gaggcgtgaa 420 ttcaaaacca
cggatcccac ctacagcagg ttcatacagt ggcagataag gaagctgagg 480
gaccttggcc tcgtaaggaa gggcgcccat cctgttaagt actgccctga atgtgaaaac
540 cctgtgggtg accatgacct ccttgagggt gagggggttg ccataaacca
gctcacactc 600 ctcaaattca aacttggaga ctcatacctg gtcgcagcca
ccttcaggcc cgagacaatc 660 tatggggcca ccaacctctg gctgaaccct
gatgaggatt atgtgagggt tgaaacaggt 720 ggtgaggagt ggataataag
cagggctgcc gtggataatc tttcacacca gaaactggac 780 ctcaaggttt
ccggtgacgt caaccccggg gacctgatag ggatgtgcgt ggagaatcct 840
gtgacgggcc aggaacaccc catactcccg gcttccttcg ttgaccctga atatgccaca
900 ggtgttgtgt tctctgtccc tgcacatgcc cctgcagact tcatagccct
tgaggacctc 960 aggacagacc atgaactcct tgaaaggtac ggtcttgagg
atgtggttgc tgatattgag 1020 cccgtgaatg tcatagcagt ggatggctac
ggtgagttcc cggcggccga ggttatagag 1080 aaatttggtg tcagaaacca
ggaggacccc cgccttgagg atgccaccgg ggagctatac 1140 aagatcgagc
atgcgagggg tgttatgagc agccacatcc ctgtctatgg tggtatgaag 1200
gtctctgagg cccgtgaggt catcgctgat gaactgaagg accagggcct tgcagatgag
1260 atgtatgaat tcgctgagcg acctgttata tgccgctgcg gtggcaggtg
cgttgtgagg 1320 gtcatggagg accagtggtt catgaagtac tctgatgacg
cctggaagga cctcgcccac 1380 aggtgcctcg atggcatgaa gataataccc
gaggaggtcc gggccaactt tgaatactac 1440 atcgactggc tcaatgactg
ggcatgttca aggaggatag gccttggaac aaggctgccc 1500 tgggatgaga
ggtggatcat cgaacccctc acagactcaa caatctacat ggcatattac 1560
accatcgcac accgcctcag ggagatggat gccggggaga tggacgatga gttctttgat
1620 gccatattcc tagatgattc aggaaccttt gaggatctca gggaggaatt
ccggtactgg 1680 tacccccttg actggaggct ctctgcaaag gacctcatag
gcaatcacct gacattccat 1740 atattccacc actcagccat attccctgag
tcagggtggc cccggggggc tgtggtcttt 1800 ggtatgggcc ttcttgaggg
caacaagatg tcatcctcca agggcaacgt catactcctg 1860 agggatgcca
tcgagaagca cggtgcagac gtggtgcggc tcttcctcat gtcctcagca 1920
gagccatggc aggactttga ctggagggag agtgaggtca tcgggacccg caggaggatt
1980 gaatggttca gggaattcgg agagagggtc tcaggtatcc tggatggtag
gccagtcctc 2040 agtgaggtta ctccagctga acctgaaagc ttcattggaa
ggtggatgat gggtcagctg 2100 aaccagagga tacgtgaagc cacaagggcc
cttgaatcat tccagacaag aaaggcagtt 2160 caggaggcac tctatctcct
taaaaaggat gttgaccact accttaagcg tgttgagggt 2220 agagttgatg
atgaggttaa atctgtcctt gcaaacgttc tgcacgcctg gataaggctc 2280
atggctccat tcatacccta cactgctgag gagatgtggg agaggtatgg tggtgagggt
2340 tttgtagcag aagctccatg gcctgacttc tcagatgatg cagagagcag
ggatgtgcag 2400 gttgcagagg agatggtcca gaataccgtt agagacattc
aggaaatcat gaagatcctt 2460 ggatccaccc cggagagggt ccacatatac
acctcaccaa aatggaaatg ggatgtgcta 2520 agggtcgcag cagaggtagg
aaaactagat atgggctcca taatgggaag ggtttcagct 2580 gagggcatcc
atgataacat gaaggaggtt gctgaatttg taaggaggat catcagggac 2640
cttggtaaat cagaggttac ggtgatagac gagtacagcg tactcatgga tgcatctgat
2700 tacattgaat cagaggttgg agccagggtt gtgatacaca gcaaaccaga
ctatgaccct 2760 gaaaacaagg ctgtgaatgc cgttcccctg aagccagcca
tataccttga atga 2814 35 306 PRT Methanococcus jannaschii 35 Met Asp
Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15
Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Gln 20
25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu
Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp
Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln
Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn
Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val
Tyr Gly Ser Thr Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn
Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg
Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys
Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Ala Ile His 145 150
155 160 Tyr Pro Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys
Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val
Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly
Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp
Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys
Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile
Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro
Glu Lys Phe Gly Gly Asp Leu Thr Val Ser Ser Tyr Glu Glu 260 265 270
Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275
280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg
Lys 290 295 300 Arg Leu 305 36 255 PRT Methanococcus jannaschii 36
Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5
10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala
Leu 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His
Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly
Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu
Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp
Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys
Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr
Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg
Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135
140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Ala His
145 150 155 160 Tyr Gln Gly Val Asp Val Val Val Gly Gly Met Glu Gln
Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys
Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly
Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val
Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala
Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met
Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile 245 250 255 37
306 PRT Methanococcus jannaschii 37 Met Asp Glu Phe Glu Met Ile Lys
Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu
Val Leu Lys Lys Asp Glu Lys Ser Ala Gly 20 25 30 Ile Gly Phe Glu
Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys
Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60
Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65
70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu
Ala Met 85 90 95 Gly Leu Lys Ala Lys Cys Ala Tyr Gly Ser Pro Phe
Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala
Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu
Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile
Tyr Pro Ile Met Gln Val Asn Gly Tyr His 145 150 155 160 Tyr Leu Gly
Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His
Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185
190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser
195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile
Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val
Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu
Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly
Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe
Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val
Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg
Leu 305 38 306 PRT Methanococcus jannaschii 38 Met Asp Glu Phe Glu
Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu
Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Gln 20 25 30 Ile
Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40
45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile
50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu
Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val
Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser
Pro Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg
Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met
Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu
Val Ile Tyr Pro Ile Met Gln Val Asn Cys Ser His 145 150 155 160 Tyr
Tyr Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170
175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His
180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser
Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu
Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly
Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr
Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe
Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser
Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn
Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295
300 Arg Leu 305 39 306 PRT Methanococcus jannaschii 39 Met Asp Glu
Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu
Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Thr 20 25
30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln
35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile
Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys
Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys
Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr
Gly Ser Thr Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val
Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg
Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val
Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Leu His 145 150 155
160 Tyr Ala Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile
165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys
Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys
Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser
Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro
Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala
Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu
Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu
Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280
285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys
290 295 300 Arg Leu 305 40 306 PRT Methanococcus jannaschii 40 Met
Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10
15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala His
20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr
Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe
Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr
Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135
140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Arg Pro His
145 150 155 160 Tyr Leu Gly Val Asp Val Ala Val Gly Gly Met Glu Gln
Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys
Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly
Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val
Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala
Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met
Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255
Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260
265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu
Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro
Ile Arg Lys 290 295 300 Arg Leu 305 41 306 PRT Methanococcus
jannaschii 41 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu
Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp
Glu Lys Ser Ala Gln 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile
His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly
Leu Lys Ala Lys Tyr Val Tyr Gly Ser Pro Phe Gln Leu Asp Lys 100 105
110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys
115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu
Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val
Asn Gln Ser His 145 150 155 160 Tyr Asp Gly Val Asp Val Ala Val Gly
Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu
Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr
Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn
Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys
Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230
235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile
Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser
Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His
Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys
Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 42 306 PRT
Methanococcus jannaschii 42 Met Asp Glu Phe Glu Met Ile Lys Arg Asn
Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Ser 20 25 30 Ile Gly Phe Glu Pro Ser
Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met
Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu
Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80
Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85
90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp
Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr
Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg
Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile
Met Gln Val Asn Thr Tyr His 145 150 155 160 Tyr Ala Gly Val Asp Val
Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala
Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro
Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205
Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210
215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 43
306 PRT Methanococcus jannaschii 43 Met Asp Glu Phe Glu Met Ile Lys
Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu
Val Leu Lys Lys Asp Glu Lys Ser Ala Pro 20 25 30 Ile Gly Phe Glu
Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys
Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60
Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65
70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu
Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Met Phe
Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala
Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu
Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile
Tyr Pro Ile Met Gln Val Asn Asn Thr His 145 150 155 160 Tyr Gly Gly
Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His
Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185
190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser
195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile
Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val
Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu
Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly
Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe
Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val
Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg
Leu 305 44 306 PRT Methanococcus jannaschii 44 Met Asp Glu Phe Glu
Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu
Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Thr 20 25 30 Ile
Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40
45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile
50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu
Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val
Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser
His Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg
Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met
Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu
Val Ile Tyr Pro Ile Met Gln Val Asn Gln Thr His 145 150 155 160 Tyr
Glu Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170
175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His
180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser
Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu
Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly
Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr
Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe
Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser
Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn
Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295
300 Arg Leu 305 45 306 PRT Methanococcus jannaschii 45 Met Asp Glu
Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu
Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala His 20 25
30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln
35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile
Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys
Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys
Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr
Gly Ser Lys Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val
Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg
Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val
Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Cys His 145 150 155
160 Tyr His Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile
165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys
Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys
Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser
Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro
Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala
Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu
Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu
Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280
285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys
290 295 300 Arg Leu 305 46 306 PRT Methanococcus jannaschii 46 Met
Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10
15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Ala
20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr
Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe
Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr
Val Tyr Gly Ser Arg Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140
Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Val Tyr His 145
150 155 160 Tyr Asp Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg
Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val
Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu
Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp
Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr
Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu
Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg
Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265
270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys
275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile
Arg Lys 290 295 300 Arg Leu 305 47 306 PRT Methanococcus jannaschii
47 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser
1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser
Ala Gly 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly
His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala
Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr
Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly
Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala
Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp Lys 100 105 110 Asp Tyr
Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125
Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130
135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Thr Tyr
Tyr 145 150 155 160 Tyr Leu Gly Val Asp Val Ala Val Gly Gly Met Glu
Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys
Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp
Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala
Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys
Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile
Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250
255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu
260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp
Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu
Pro Ile Arg Lys 290 295 300 Arg Leu 305 48 306 PRT Methanococcus
jannaschii 48 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu
Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp
Glu Lys Ser Ala Leu 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile
His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly
Leu Lys Ala Lys Tyr Val Tyr Gly Ser Pro Phe Gln Leu Asp Lys 100 105
110
Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115
120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn
Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn
Gln Ile His 145 150 155 160 Ser Ser Gly Val Asp Val Ala Val Gly Gly
Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu
Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly
Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe
Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile
Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235
240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys
245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr
Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro
Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile
Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 49 306 PRT
Methanococcus jannaschii 49 Met Asp Glu Phe Glu Met Ile Lys Arg Asn
Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Asp 20 25 30 Ile Gly Phe Glu Pro Ser
Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met
Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu
Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80
Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85
90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp
Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr
Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg
Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile
Met Gln Val Asn Gly Met His 145 150 155 160 Tyr Gln Gly Val Asp Val
Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala
Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro
Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205
Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210
215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 50
306 PRT Methanococcus jannaschii 50 Met Asp Glu Phe Glu Met Ile Lys
Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu
Val Leu Lys Lys Asp Glu Lys Ser Ala Tyr 20 25 30 Ile Gly Phe Glu
Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys
Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60
Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65
70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu
Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Leu Phe
Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala
Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu
Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile
Tyr Pro Ile Met Gln Val Asn Asp Ile His 145 150 155 160 Tyr Thr Gly
Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His
Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185
190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser
195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile
Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val
Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu
Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly
Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe
Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val
Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg
Leu 305 51 306 PRT Methanococcus jannaschii 51 Met Asp Glu Phe Glu
Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu
Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Leu 20 25 30 Ile
Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40
45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile
50 55 60 Leu Leu Thr Asp Leu Asn Ala Tyr Leu Asn Gln Lys Gly Glu
Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val
Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser
Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg
Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met
Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu
Val Ile Tyr Pro Ile Met Gln Val Asn Asp Ile His 145 150 155 160 Tyr
Leu Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170
175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His
180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser
Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu
Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly
Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr
Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe
Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser
Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn
Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295
300 Arg Leu 305 52 306 PRT Methanococcus jannaschii 52 Met Asp Glu
Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu
Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Leu 20 25
30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln
35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile
Ile Ile 50 55 60 Leu Leu Thr Asp Leu Lys Ala Tyr Leu Asn Gln Lys
Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys
Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr
Gly Ser Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val
Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg
Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val
Ala Glu Val Ile Tyr Pro Ile Met Ser Val Asn Val Ile His 145 150 155
160 Tyr Leu Gly Val Asp Val Val Val Gly Gly Met Glu Gln Arg Lys Ile
165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys
Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys
Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser
Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro
Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala
Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu
Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu
Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280
285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys
290 295 300 Arg Leu 305 53 306 PRT Methanococcus jannaschii 53 Met
Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10
15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Leu
20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr
Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe
Asp Ile Ile Ile 50 55 60 Leu Leu Pro Asp Leu Ser Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr
Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140
Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Asp Ile His 145
150 155 160 Tyr Leu Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg
Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val
Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu
Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp
Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr
Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu
Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg
Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265
270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys
275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile
Arg Lys 290 295 300 Arg Leu 305 54 306 PRT Methanococcus jannaschii
54 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser
1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser
Ala Thr 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly
His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala
Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr
Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly
Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala
Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105 110 Asp Tyr
Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125
Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130
135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Asp Ile
His 145 150 155 160 Tyr Ala Gly Val Asp Val Ala Val Gly Gly Met Glu
Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys
Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp
Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala
Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys
Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile
Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250
255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu
260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp
Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu
Pro Ile Arg Lys 290 295 300 Arg Leu 305 55 306 PRT Methanococcus
jannaschii 55 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu
Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp
Glu Lys Ser Ala Thr 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile
His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ser Asp Leu
Pro Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly
Leu Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105
110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys
115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu
Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val
Asn Asp Ile His 145 150 155 160 Tyr Leu Gly Val Asp Val Ala Val Gly
Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu
Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr
Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn
Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys
Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230
235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile
Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser
Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His
Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys
Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 56 306 PRT
Methanococcus jannaschii 56 Met Asp Glu Phe Glu Met Ile Lys Arg Asn
Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Thr 20 25 30 Ile Gly Phe Glu Pro Ser
Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met
Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu
Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80
Glu Ile Arg Lys Ile Gly Asp
Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys
Tyr Val Tyr Gly Ser Met Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr
Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg
Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135
140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Ser Ser His
145 150 155 160 Tyr Asp Gly Val Asp Val Ala Val Gly Gly Met Glu Gln
Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys
Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly
Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val
Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala
Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met
Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255
Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260
265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu
Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro
Ile Arg Lys 290 295 300 Arg Leu 305 57 306 PRT Methanococcus
jannaschii 57 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu
Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp
Glu Lys Ser Ala Gln 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile
His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Pro Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly
Leu Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys 100 105
110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys
115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu
Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val
Asn Asp Ile His 145 150 155 160 Tyr Leu Gly Val Asp Val Asp Val Gly
Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu
Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr
Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn
Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys
Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230
235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile
Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser
Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His
Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys
Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 58 306 PRT
Methanococcus jannaschii 58 Met Asp Glu Phe Glu Met Ile Lys Arg Asn
Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala His 20 25 30 Ile Gly Phe Glu Pro Ser
Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met
Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu
Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80
Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85
90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Ala Phe Gln Leu Asp
Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr
Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg
Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile
Met Gln Val Asn Gly His His 145 150 155 160 Tyr Ile Gly Val Asp Val
Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His Met Leu Ala
Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185 190 Asn Pro
Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser 195 200 205
Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210
215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg Leu 305 59
306 PRT Methanococcus jannaschii 59 Met Asp Glu Phe Glu Met Ile Lys
Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu
Val Leu Lys Lys Asp Glu Lys Ser Ala Tyr 20 25 30 Ile Gly Phe Glu
Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys
Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile 50 55 60
Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp 65
70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu
Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Ala Phe
Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala
Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met Glu Leu
Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu Val Ile
Tyr Pro Ile Met Gln Val Asn Cys Ala His 145 150 155 160 Tyr Leu Gly
Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170 175 His
Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His 180 185
190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser
195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile
Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val
Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr Phe Leu
Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe Gly Gly
Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser Leu Phe
Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn Ala Val
Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295 300 Arg
Leu 305 60 306 PRT Methanococcus jannaschii 60 Met Asp Glu Phe Glu
Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu Glu Glu
Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Gly 20 25 30 Ile
Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln 35 40
45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile
50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu
Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val
Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser
Ser Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val Tyr Arg
Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg Ser Met
Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val Ala Glu
Val Ile Tyr Pro Ile Met Gln Val Asn Thr Ser His 145 150 155 160 Tyr
Leu Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile 165 170
175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His
180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser
Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu
Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly
Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala Lys Tyr
Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu Lys Phe
Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu Glu Ser
Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280 285 Asn
Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys 290 295
300 Arg Leu 305 61 306 PRT Methanococcus jannaschii 61 Met Asp Glu
Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10 15 Glu
Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Thr 20 25
30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln
35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile
Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys
Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys
Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr Val Tyr
Gly Ser Asn Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu Asn Val
Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala Arg Arg
Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140 Lys Val
Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Leu His 145 150 155
160 Tyr Gln Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile
165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys
Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys
Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp Asp Ser
Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr Cys Pro
Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu Ile Ala
Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg Pro Glu
Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265 270 Leu
Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys 275 280
285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys
290 295 300 Arg Leu 305 62 306 PRT Methanococcus jannaschii 62 Met
Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser 1 5 10
15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Thr
20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr
Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe
Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr
Val Tyr Gly Ser Ser Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140
Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Leu His 145
150 155 160 Tyr Gln Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg
Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val
Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu
Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp
Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr
Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu
Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg
Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265
270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys
275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile
Arg Lys 290 295 300 Arg Leu 305 63 306 PRT Methanococcus jannaschii
63 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser
1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser
Ala Leu 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly
His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu Gln Asn Ala
Gly Phe Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr
Leu Asn Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly
Asp Tyr Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala
Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp Lys 100 105 110 Asp Tyr
Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125
Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130
135 140 Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Val
His 145 150 155 160 Tyr Gln Gly Val Asp Val Ala Val Gly Gly Met Glu
Gln Arg Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys
Lys Val Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp
Gly Glu Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala
Val Asp Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys
Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile
Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250
255 Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu
260 265 270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp
Leu Lys 275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu
Pro Ile Arg Lys 290 295 300 Arg Leu 305 64 306 PRT Methanococcus
jannaschii 64 Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu
Ile Ile Ser 1 5 10 15 Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp
Glu Lys Ser Ala Thr 20 25 30 Ile Gly Phe Glu Pro Ser Gly Lys Ile
His Leu Gly His Tyr Leu Gln 35 40 45 Ile Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe
Asp Ile Ile Ile 50 55 60 Leu Leu Ala Asp Leu His Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp 65 70 75 80 Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met 85 90 95 Gly Leu Lys Ala Lys Tyr
Val Tyr Gly Ser Ser Phe Gln Leu Asp Lys 100 105 110 Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys 115 120 125 Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro 130 135 140
Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Pro Ser His 145
150 155 160 Tyr Gln Gly Val Asp Val Ala Val Gly Gly Met Glu Gln Arg
Lys Ile 165 170 175 His Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val
Val Cys Ile His 180 185 190 Asn Pro Val Leu Thr Gly Leu Asp Gly Glu
Gly Lys Met Ser Ser Ser 195 200 205 Lys Gly Asn Phe Ile Ala Val Asp
Asp Ser Pro Glu Glu Ile Arg Ala 210 215 220 Lys Ile Lys Lys Ala Tyr
Cys Pro Ala Gly Val Val Glu Gly Asn Pro 225 230 235 240 Ile Met Glu
Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys 245 250 255 Arg
Pro Glu Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu 260 265
270 Leu Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys
275 280 285 Asn Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile
Arg Lys 290 295 300 Arg Leu 305 65 932 PRT Archaeoglobus fulgidus
65 Met Ser Asp Phe Arg Ile Ile Glu Glu Lys Trp Gln Lys Ala Trp Glu
1 5 10 15 Lys Asp Arg Ile Phe Glu Ser Asp Pro Asn Glu Lys Glu Lys
Phe Phe 20 25 30 Leu Thr Ile Pro Tyr Pro Tyr Leu Asn Gly Asn Leu
His Ala Gly His 35 40 45 Thr Arg Thr Phe Thr Ile Gly Asp Ala Phe
Ala Arg Tyr Met Arg Met 50 55 60 Lys Gly Tyr Asn Val Leu Phe Pro
Leu Gly Phe His Val Thr Gly Thr 65 70 75 80 Pro Ile Ile Gly Leu Ala
Glu Leu Ile Ala Lys Arg Asp Glu Arg Thr 85 90 95 Ile Glu Val Tyr
Thr Lys Tyr His Asp Val Pro Leu Glu Asp Leu Leu 100 105 110 Gln Leu
Thr Thr Pro Glu Lys Ile Val Glu Tyr Phe Ser Arg Glu Ala 115 120 125
Leu Gln Ala Leu Lys Ser Ile Gly Tyr Ser Ile Asp Trp Arg Arg Val 130
135 140 Phe Thr Thr Thr Asp Glu Glu Tyr Gln Arg Phe Ile Glu Trp Gln
Tyr 145 150 155 160 Trp Lys Leu Lys Glu Leu Gly Leu Ile Val Lys Gly
Thr His Pro Val 165 170 175 Arg Tyr Cys Pro His Asp Gln Asn Pro Val
Glu Asp His Asp Leu Leu 180 185 190 Ala Gly Glu Glu Ala Thr Ile Val
Glu Phe Thr Val Ile Lys Phe Arg 195 200 205 Leu Glu Asp Gly Asp Leu
Ile Phe Pro Cys Ala Thr Leu Arg Pro Glu 210 215 220 Thr Val Phe Gly
Val Thr Asn Ile Trp Val Lys Pro Thr Thr Tyr Val 225 230 235 240 Ile
Ala Glu Val Asp Gly Glu Lys Trp Phe Val Ser Lys Glu Ala Tyr 245 250
255 Glu Lys Leu Thr Tyr Thr Glu Lys Lys Val Arg Leu Leu Glu Glu Val
260 265 270 Asp Ala Ser Gln Phe Phe Gly Lys Tyr Val Ile Val Pro Leu
Val Asn 275 280 285 Arg Lys Val Pro Ile Leu Pro Ala Glu Phe Val Asp
Thr Asp Asn Ala 290 295 300 Thr Gly Val Val Met Ser Val Pro Ala His
Ala Pro Phe Asp Leu Ala 305 310 315 320 Ala Ile Glu Asp Leu Lys Arg
Asp Glu Glu Thr Leu Ala Lys Tyr Gly 325 330 335 Ile Asp Lys Ser Val
Val Glu Ser Ile Lys Pro Ile Val Leu Ile Lys 340 345 350 Thr Asp Ile
Glu Gly Val Pro Ala Glu Lys Leu Ile Arg Glu Leu Gly 355 360 365 Val
Lys Ser Gln Lys Asp Lys Glu Leu Leu Asp Lys Ala Thr Lys Thr 370 375
380 Leu Tyr Lys Lys Glu Tyr His Thr Gly Ile Met Leu Asp Asn Thr Met
385 390 395 400 Asn Tyr Ala Gly Met Lys Val Ser Glu Ala Lys Glu Arg
Val His Glu 405 410 415 Asp Leu Val Lys Leu Gly Leu Gly Asp Val Phe
Tyr Glu Phe Ser Glu 420 425 430 Lys Pro Val Ile Cys Arg Cys Gly Thr
Lys Cys Val Val Lys Val Val 435 440 445 Arg Asp Gln Trp Phe Leu Asn
Tyr Ser Asn Arg Glu Trp Lys Glu Lys 450 455 460 Val Leu Asn His Leu
Glu Lys Met Arg Ile Ile Pro Asp Tyr Tyr Lys 465 470 475 480 Glu Glu
Phe Arg Asn Lys Ile Glu Trp Leu Arg Asp Lys Ala Cys Ala 485 490 495
Arg Arg Lys Gly Leu Gly Thr Arg Ile Pro Trp Asp Lys Glu Trp Leu 500
505 510 Ile Glu Ser Leu Ser Asp Ser Thr Ile Tyr Met Ala Tyr Tyr Ile
Leu 515 520 525 Ala Lys Tyr Ile Asn Ala Gly Leu Leu Lys Ala Glu Asn
Met Thr Pro 530 535 540 Glu Phe Leu Asp Tyr Val Leu Leu Gly Lys Gly
Glu Val Gly Lys Val 545 550 555 560 Ala Glu Ala Ser Lys Leu Ser Val
Glu Leu Ile Gln Gln Ile Arg Asp 565 570 575 Asp Phe Glu Tyr Trp Tyr
Pro Val Asp Leu Arg Ser Ser Gly Lys Asp 580 585 590 Leu Val Ala Asn
His Leu Leu Phe Tyr Leu Phe His His Val Ala Ile 595 600 605 Phe Pro
Pro Asp Lys Trp Pro Arg Ala Ile Ala Val Asn Gly Tyr Val 610 615 620
Ser Leu Glu Gly Lys Lys Met Ser Lys Ser Lys Gly Pro Leu Leu Thr 625
630 635 640 Met Lys Arg Ala Val Gln Gln Tyr Gly Ala Asp Val Thr Arg
Leu Tyr 645 650 655 Ile Leu His Ala Ala Glu Tyr Asp Ser Asp Ala Asp
Trp Lys Ser Arg 660 665 670 Glu Val Glu Gly Leu Ala Asn His Leu Arg
Arg Phe Tyr Asn Leu Val 675 680 685 Lys Glu Asn Tyr Leu Lys Glu Val
Gly Glu Leu Thr Thr Leu Asp Arg 690 695 700 Trp Leu Val Ser Arg Met
Gln Arg Ala Ile Lys Glu Val Arg Glu Ala 705 710 715 720 Met Asp Asn
Leu Gln Thr Arg Arg Ala Val Asn Ala Ala Phe Phe Glu 725 730 735 Leu
Met Asn Asp Val Arg Trp Tyr Leu Arg Arg Gly Gly Glu Asn Leu 740 745
750 Ala Ile Ile Leu Asp Asp Trp Ile Lys Leu Leu Ala Pro Phe Ala Pro
755 760 765 His Ile Cys Glu Glu Leu Trp His Leu Lys His Asp Ser Tyr
Val Ser 770 775 780 Leu Glu Ser Tyr Pro Glu Tyr Asp Glu Thr Arg Val
Asp Glu Glu Ala 785 790 795 800 Glu Arg Ile Glu Glu Tyr Leu Arg Asn
Leu Val Glu Asp Ile Gln Glu 805 810 815 Ile Lys Lys Phe Val Ser Asp
Ala Lys Glu Val Tyr Ile Ala Pro Ala 820 825 830 Glu Asp Trp Lys Val
Lys Ala Ala Lys Val Val Ala Glu Ser Gly Asp 835 840 845 Val Gly Glu
Ala Met Lys Gln Leu Met Gln Asp Glu Glu Leu Arg Lys 850 855 860 Leu
Gly Lys Glu Val Ser Asn Phe Val Lys Lys Ile Phe Lys Asp Arg 865 870
875 880 Lys Lys Leu Met Leu Val Lys Glu Trp Glu Val Leu Gln Gln Asn
Leu 885 890 895 Lys Phe Ile Glu Asn Glu Thr Gly Leu Lys Val Ile Leu
Asp Thr Gln 900 905 910 Arg Val Pro Glu Glu Lys Arg Arg Gln Ala Val
Pro Gly Lys Pro Ala 915 920 925 Ile Tyr Val Ala 930 66 937 PRT
Methanobacterium thermoautotrophicum 66 Val Asp Ile Glu Arg Lys Trp
Arg Asp Arg Trp Arg Asp Ala Gly Ile 1 5 10 15 Phe Gln Ala Asp Pro
Asp Asp Arg Glu Lys Ile Phe Leu Thr Val Ala 20 25 30 Tyr Pro Tyr
Pro Ser Gly Ala Met His Ile Gly His Gly Arg Thr Tyr 35 40 45 Thr
Val Pro Asp Val Tyr Ala Arg Phe Lys Arg Met Gln Gly Tyr Asn 50 55
60 Val Leu Phe Pro Met Ala Trp His Val Thr Gly Ala Pro Val Ile Gly
65 70 75 80 Ile Ala Arg Arg Ile Gln Arg Lys Asp Pro Trp Thr Leu Lys
Ile Tyr 85 90 95 Arg Glu Val His Arg Val Pro Glu Asp Glu Leu Glu
Arg Phe Ser Asp 100 105 110 Pro Glu Tyr Ile Val Glu Tyr Phe Ser Arg
Glu Tyr Arg Ser Val Met 115 120 125 Glu Asp Met Gly Tyr Ser Ile Asp
Trp Arg Arg Glu Phe Lys Thr Thr 130 135 140 Asp Pro Thr Tyr Ser Arg
Phe Ile Gln Trp Gln Ile Arg Lys Leu Arg 145 150 155 160 Asp Leu Gly
Leu Val Arg Lys Gly Ala His Pro Val Lys Tyr Cys Pro 165 170 175 Glu
Cys Glu Asn Pro Val Gly Asp His Asp Leu Leu Glu Gly Glu Gly 180 185
190 Val Ala Ile Asn Gln Leu Thr Leu Leu Lys Phe Lys Leu Gly Asp Ser
195 200 205 Tyr Leu Val Ala Ala Thr Phe Arg Pro Glu Thr Ile Tyr Gly
Ala Thr 210 215 220 Asn Leu Trp Leu Asn Pro Asp Glu Asp Tyr Val Arg
Val Glu Thr Gly 225 230 235 240 Gly Glu Glu Trp Ile Ile Ser Arg Ala
Ala Val Asp Asn Leu Ser His 245 250 255 Gln Lys Leu Asp Leu Lys Val
Ser Gly Asp Val Asn Pro Gly Asp Leu 260 265 270 Ile Gly Met Cys Val
Glu Asn Pro Val Thr Gly Gln Glu His Pro Ile 275 280 285 Leu Pro Ala
Ser Phe Val Asp Pro Glu Tyr Ala Thr Gly Val Val Phe 290 295 300 Ser
Val Pro Ala His Ala Pro Ala Asp Phe Ile Ala Leu Glu Asp Leu 305 310
315 320 Arg Thr Asp His Glu Leu Leu Glu Arg Tyr Gly Leu Glu Asp Val
Val 325 330 335 Ala Asp Ile Glu Pro Val Asn Val Ile Ala Val Asp Gly
Tyr Gly Glu 340 345 350 Phe Pro Ala Ala Glu Val Ile Glu Lys Phe Gly
Val Arg Asn Gln Glu 355 360 365 Asp Pro Arg Leu Glu Asp Ala Thr Gly
Glu Leu Tyr Lys Ile Glu His 370 375 380 Ala Arg Gly Val Met Ser Ser
His Ile Pro Val Tyr Gly Gly Met Lys 385 390 395 400 Val Ser Glu Ala
Arg Glu Val Ile Ala Asp Glu Leu Lys Asp Gln Gly 405 410 415 Leu Ala
Asp Glu Met Tyr Glu Phe Ala Glu Arg Pro Val Ile Cys Arg 420 425 430
Cys Gly Gly Arg Cys Val Val Arg Val Met Glu Asp Gln Trp Phe Met 435
440 445 Lys Tyr Ser Asp Asp Ala Trp Lys Asp Leu Ala His Arg Cys Leu
Asp 450 455 460 Gly Met Lys Ile Ile Pro Glu Glu Val Arg Ala Asn Phe
Glu Tyr Tyr 465 470 475 480 Ile Asp Trp Leu Asn Asp Trp Ala Cys Ser
Arg Arg Ile Gly Leu Gly 485 490 495 Thr Arg Leu Pro Trp Asp Glu Arg
Trp Ile Ile Glu Pro Leu Thr Asp 500 505 510 Ser Thr Ile Tyr Met Ala
Tyr Tyr Thr Ile Ala His Arg Leu Arg Glu 515 520 525 Met Asp Ala Gly
Glu Met Asp Asp Glu Phe Phe Asp Ala Ile Phe Leu 530 535 540 Asp Asp
Ser Gly Thr Phe Glu Asp Leu Arg Glu Glu Phe Arg Tyr Trp 545 550 555
560 Tyr Pro Leu Asp Trp Arg Leu Ser Ala Lys Asp Leu Ile Gly Asn His
565 570 575 Leu Thr Phe His Ile Phe His His Ser Ala Ile Phe Pro Glu
Ser Gly 580 585 590 Trp Pro Arg Gly Ala Val Val Phe Gly Met Gly Leu
Leu Glu Gly Asn 595 600 605 Lys Met Ser Ser Ser Lys Gly Asn Val Ile
Leu Leu Arg Asp Ala Ile 610 615 620 Glu Lys His Gly Ala Asp Val Val
Arg Leu Phe Leu Met Ser Ser Ala 625 630 635 640 Glu Pro Trp Gln Asp
Phe Asp Trp Arg Glu Ser Glu Val Ile Gly Thr 645 650 655 Arg Arg Arg
Ile Glu Trp Phe Arg Glu Phe Gly Glu Arg Val Ser Gly 660 665 670 Ile
Leu Asp Gly Arg Pro Val Leu Ser Glu Val Thr Pro Ala Glu Pro 675 680
685 Glu Ser Phe Ile Gly Arg Trp Met Met Gly Gln Leu Asn Gln Arg Ile
690 695 700 Arg Glu Ala Thr Arg Ala Leu Glu Ser Phe Gln Thr Arg Lys
Ala Val 705 710 715 720 Gln Glu Ala Leu Tyr Leu Leu Lys Lys Asp Val
Asp His Tyr Leu Lys 725 730 735 Arg Val Glu Gly Arg Val Asp Asp Glu
Val Lys Ser Val Leu Ala Asn 740 745 750 Val Leu His Ala Trp Ile Arg
Leu Met Ala Pro Phe Ile Pro Tyr Thr 755 760 765 Ala Glu Glu Met Trp
Glu Arg Tyr Gly Gly Glu Gly Phe Val Ala Glu 770 775 780 Ala Pro Trp
Pro Asp Phe Ser Asp Asp Ala Glu Ser Arg Asp Val Gln 785 790 795 800
Val Ala Glu Glu Met Val Gln Asn Thr Val Arg Asp Ile Gln Glu Ile 805
810 815 Met Lys Ile Leu Gly Ser Thr Pro Glu Arg Val His Ile Tyr Thr
Ser 820 825 830 Pro Lys Trp Lys Trp Asp Val Leu Arg Val Ala Ala Glu
Val Gly Lys 835 840 845 Leu Asp Met Gly Ser Ile Met Gly Arg Val Ser
Ala Glu Gly Ile His 850 855 860 Asp Asn Met Lys Glu Val Ala Glu Phe
Val Arg Arg Ile Ile Arg Asp 865 870 875 880 Leu Gly Lys Ser Glu Val
Thr Val Ile Asp Glu Tyr Ser Val Leu Met 885 890 895 Asp Ala Ser Asp
Tyr Ile Glu Ser Glu Val Gly Ala Arg Val Val Ile 900 905 910 His Ser
Lys Pro Asp Tyr Asp Pro Glu Asn Lys Ala Val Asn Ala Val 915 920 925
Pro Leu Lys Pro Ala Ile Tyr Leu Glu 930 935 67 30 DNA Artificial
Sequence synthetic oligonucleotide 67 atgcatgctg cattaatgaa
tcggccaacg 30 68 27 DNA Artificial Sequence synthetic
oligonucleotide 68 tccccgcgga ggtggcactt ttcgggg 27 69 28 DNA
Artificial Sequence synthetic oligonucleotide 69 ggaattccat
taggacgaat ttgaaatg 28 70 33 DNA Artificial Sequence synthetic
oligonucleotide 70 aaactgcagt tataatctct ttctaattgg ctc 33 71 10
DNA Artificial Sequence synthetic oligonucleotide 71 aaaactgcag 10
72 10 DNA Artificial Sequence synthetic oligonucleotide 72
aaaactgcag 10 73 28 DNA Artificial Sequence synthetic
oligonucleotide 73 ggaattccat atggacgaat ttgaaatg 28 74 69 DNA
Artificial Sequence synthetic oligonucleotide 74 gtattttacc
acttggttca aaacctatmn nagcagattt ttcatctttt tttcatcttt 60 ttttaaaac
69 75 27 DNA Artificial Sequence synthetic oligonucleotide 75
taggttttga accaagtggt aaaatac 27 76 62 DNA Artificial Sequence
synthetic oligonucleotide 76 cattcagtgt ataatcctta tcaagctgga
amnnacttcc ataaacatat tttgccttta 60 ac 62 77 30 DNA Artificial
Sequence synthetic oligonucleotide 77 tccagcttga taaggattat
acactgaatg 30 78 69 DNA Artificial Sequence synthetic
oligonucleotide 78 catccctcca actgcaacat caacgccmnn ataatgmnnm
nnattaacct gcattattgg 60 atagataac 69 79 26 DNA Artificial Sequence
synthetic oligonucleotide 79 gcgttgatgt tgcagttgga gggatg 26 80 4
PRT Methanococcus jannaschii 80 Ala Asp Leu His 1 81 13 PRT
Methanococcus jannaschii 81 Gln Val Asn Asp Ile His Tyr Leu Gly Val
Asp Val Ala 1 5 10 82 13 PRT Methanococcus jannaschii MISC_FEATURE
(4)..(5) any 82 Gln Val Asn Xaa
Xaa His Tyr Xaa Gly Val Asp Val Ala 1 5 10 83 13 PRT Methanococcus
jannaschii MISC_FEATURE (4)..(5) any 83 Gln Val Asn Xaa Xaa His Tyr
Xaa Gly Val Asp Val Xaa 1 5 10 84 13 PRT Methanococcus jannaschii
MISC_FEATURE (1)..(1) any 84 Xaa Val Asn Xaa Ile His Tyr Leu Gly
Val Asp Val Xaa 1 5 10 85 4 PRT Artificial Sequence consensus
sequence from pentafluorophenylalanine selection 85 Gln Asp Leu Tyr
1 86 13 PRT Artificial Sequence consensus sequence from
pentafluorophenylalanin- e selection 86 Ala Val Asn Ala Ile His Tyr
Leu Gly Val Asp Val Leu 1 5 10 87 44 PRT Escherichia coli 87 Trp
Phe Gly Asn Met Asn Val Leu Thr Phe Leu Arg Asp Ile Gly Lys 1 5 10
15 His Phe Ser Val Asn Gln Met Ile Asn Lys Glu Ala Val Lys Gln Arg
20 25 30 Leu Asn Arg Glu Asp Gln Gly Ile Ser Phe Thr Glu 35 40 88
39 PRT Homo sapiens 88 Leu Ser Lys Glu Tyr Thr Leu Asp Val Tyr Arg
Leu Ser Ser Val Val 1 5 10 15 Thr Gln His Asp Ser Lys Lys Ala Gly
Ala Glu Val Val Lys Gln Val 20 25 30 Glu His Pro Leu Leu Ser Gly 35
89 39 PRT Methanococcus jannaschii 89 Leu Asp Lys Asp Tyr Thr Leu
Asn Val Tyr Arg Leu Ala Leu Lys Thr 1 5 10 15 Thr Leu Lys Arg Ala
Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp 20 25 30 Glu Asn Pro
Lys Val Ala Glu 35 90 77 RNA Methanococcus jannaschii misc_feature
(33)..(34) any 90 ccggcgguag uucagccugg uagaacggcg ganncuannu
ccgcaugucg cugguucaaa 60 uccggcccgc cggacca 77 91 77 RNA
Methanococcus jannaschii misc_feature (16)..(18) any 91 ccggcgguag
uucagnnngg nagaacggcg ganucuannu ccgcangncg cugguucaan 60
nccggcccgc cggacca 77 92 77 DNA Methanococcus jannaschii 92
ccggcggtag ttcagcctgg tagaacggcg gactctagat ccgcatgtcg ctggttcaaa
60 tccggcccgc cggacca 77 93 77 DNA Methanococcus jannaschii 93
ccggcggtag ttcagcctgg tagaacggcg gacactaaat ccgcatgtcg ctggttcaaa
60 tccggcccgc cggacca 77 94 77 DNA Methanococcus jannaschii 94
ccggcggtag ttcagcctgg tagaacggcg gacactaaat ccgcatgtcg ctggttcaaa
60 tccggcctgc cggacca 77 95 77 DNA Methanococcus jannaschii 95
ccggcggtag ttcagcctgg tagaacggcg gaatctaaat ccgcatgtcg ttggttcaaa
60 tccggcccgc cggacca 77 96 77 DNA Methanococcus jannaschii 96
ccggcggtag ttcagtgagg aagaacggcg gactctaaat ccgcaaggcg ctggttcaag
60 tccggcccgc cggacca 77 97 77 DNA Methanococcus jannaschii 97
ccggcggtag ttcagcaggg cagaacggcg gactctaaat ccgcatggcg ctggttcaaa
60 tccggcccgc cggacca 77 98 77 DNA Methanococcus jannaschii 98
ccggcggtag ttcagatagg gagaacggcg gactctaact ccgcatggcg ctggttcaat
60 tccggcccgc cggacca 77 99 77 DNA Methanococcus jannaschii 99
ccggcggtag ttcaggtagg gagaacggcg gactctaact ccgcatgtcg ctggttcaag
60 tccggcccgc cggacca 77 100 77 DNA Methanococcus jannaschii 100
ccggcggtag ttcagtaggg aagaacggcg gactctaaat ccgcacgtcg ctggttcaag
60 tccggcccgc cggacca 77 101 77 DNA Methanococcus jannaschii 101
ccggcggtag ttcagggtgg gagaacggcg gagtctaggt ccgcatgccg ctggttcaat
60 accggcccgc cggacca 77 102 77 DNA Methanococcus jannaschii 102
ccggcggtag ttcagttcgg cagaacggcg gagtctatat ccgcacgccg ctggttcaac
60 cccggcccgc cggacca 77 103 77 DNA Methanococcus jannaschii 103
ccggcggtag ttcagtgtgg aagaacggcg gattctatct ccgcacggcg ctggttcaag
60 gccggcccgc cggacca 77 104 88 DNA Halobacterium sp. NRC-1 104
gcgagggtag ccaagctcgg ccaacggcga cggactcaag atccgttctc gtaggagttc
60 gagggttcga atcccttccc tcgcacca 88 105 89 DNA Halobacterium sp.
NRC-1 105 gcgagggtag ccaagctcgg ccaacggcga cggacttcct aatccgttct
cgtaggagtt 60 cgagggttcg aatcccttcc ctcgcacca 89 106 76 RNA Thermus
thermophilus 106 gcucgcguag cucagcaggu agagcacacc cuugguaagg
gugaggucgc cgguucgagc 60 ccggccgcga gcucca 76 107 76 RNA Thermus
thermophilus 107 gaucgcguag cucagcaggu agagcacacc cuugguaagg
gugaggucgc cgguucgagc 60 ccggccgcga ucucca 76 108 76 RNA Thermus
thermophilus 108 gaucgcguag cucagcaggu agagcacacc cuucuaaagg
gugaggucgc cgguucgagc 60 ccggccgcga ucucca 76
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